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From: Ziwei W. <wa...@cp...> - 2022-11-14 03:44:53
|
Hello,
Thanks for your quick reply! I made the question more clear with two screenshots here.
Sincerely,
Lilas
-----原始邮件-----
发件人:Colin <col...@gm...>
发送时间:2022-11-12 07:55:03 (星期六)
收件人: "Ziwei Wang" <wa...@cp...>
抄送: gmod-ajax <gmo...@li...>
主题: Re: [Gmod-ajax] How to parse md tag in CRAM files
In jbrowse code we use feature.get('mismatches') which works on BAM and CRAM features. Would that help your case?
-Colin
On Fri, Nov 11, 2022, 4:06 PM Ziwei Wang <wa...@cp...> wrote:
Hello,
I have BAM files and CRAM files with MD tags and need to use MD tags to filter the bases I need. When I use BAM files, everything works fine. But when I use CRAM files, there are no MD tags in Feature.record. How should I get MD tags in CRAM files? Thanks!
Sincerely,
Lilas
_______________________________________________
Gmod-ajax mailing list
Gmo...@li...
https://lists.sourceforge.net/lists/listinfo/gmod-ajax
|
|
From: Colin <col...@gm...> - 2022-11-11 23:55:22
|
In jbrowse code we use feature.get('mismatches') which works on BAM and
CRAM features. Would that help your case?
-Colin
On Fri, Nov 11, 2022, 4:06 PM Ziwei Wang <wa...@cp...> wrote:
> Hello,
>
> I have BAM files and CRAM files with MD tags and need to use MD tags
> to filter the bases I need. When I use BAM files, everything works fine.
> But when I use CRAM files, there are no MD tags in Feature.record. How
> should I get MD tags in CRAM files? Thanks!
>
> Sincerely,
>
> Lilas
> _______________________________________________
> Gmod-ajax mailing list
> Gmo...@li...
> https://lists.sourceforge.net/lists/listinfo/gmod-ajax
>
|
|
From: Ziwei W. <wa...@cp...> - 2022-11-11 07:45:16
|
Hello, I have BAM files and CRAM files with MD tags and need to use MD tags to filter the bases I need. When I use BAM files, everything works fine. But when I use CRAM files, there are no MD tags in Feature.record. How should I get MD tags in CRAM files? Thanks! Sincerely, Lilas |
|
From: Colin <col...@gm...> - 2022-10-19 21:52:40
|
In addition to other things noted, JBrowse 2 can also load data directly from Google Drive or Dropbox share links. Basically, you get a URL from "sharing" a google drive file or dropbox file, and can paste the share URL into the "Add track" widget. A screenshot is attached showing the buttons for dropbox and google drive in the "add track" widget in JBrowse 2 This assumes you are using jbrowse 2, the jbrowse 1 app is a bit different and doesn't have any google drive/dropbox support -Colin On Wed, Oct 19, 2022 at 1:29 PM Scott Cain <sc...@sc...> wrote: > The other thing that just occurred to me is relatively low-tech: get a > bunch of thumb usb drives (4 or 8 GB ones are pretty cheap) and put the > data on them and then just hand them out to your students. > > On Wed, Oct 19, 2022 at 9:19 AM Scott Cain <sc...@sc...> wrote: > >> Hi Olivia, >> >> How much control do you have over the students' learning environment? If >> you have access to the machines to set them up before the students use them >> and there aren't too many (or you had a good network admin), you could just >> place the data files on each computer's hard drive, or if the files are too >> big to do that, you could mount the one drive on each of the computers as a >> local drive (I googled for directions for how to do that and it looks like >> it would probably be doable for Windows and Mac at least). >> >> If you don't have easy access to the students' machines, then you need to >> be able to give them a URL to load data. I have had lots of success with >> Amazon Web Services S3 buckets, where I configured the bucket to allow CORS >> requests (cross origin resource sharing--required by web servers as a way >> to protect against malicious websites from getting dangerous things to your >> computer without you knowing it) and then set the data in the S3 bucket as >> publicly readable. If you want to go down that route, we can help you with >> the details, and I suspect since this is a research project involving >> teaching students, you could probably get some S3 storage space from AWS >> for free. >> >> I know that it is also possible to do all of the above (CORS, public read >> data, and a URL) with Google Cloud, but I don't know how to do it; I only >> know it's possible because I have a track in WormBase's JBrowse that pulls >> data from a researcher who put his data in a public Google Cloud space. And >> it is possible that you could do all of this with OneDrive, but I don't >> know how to do that either. >> >> The last thing you could do would be to ask the IT staff at UML to set up >> a small web server for your project where you could put the data or set one >> up yourself if you're allowed by the university; if you wanted to go down >> that route, we can help with that too. >> >> Good luck with your choice, >> Scott >> >> >> >> >> On Wed, Oct 19, 2022 at 5:45 AM Rasmussen, Olivia < >> Oli...@st...> wrote: >> >>> Hello, >>> Thanks so much for getting back to me and sorry for the delayed >>> response. This is helpful information to know. It seems like the problem is >>> definitely that it is not public. I was wondering if there is any sort of >>> work around for this? It's okay if not we are just trying to understand the >>> best way to approach this based on what we are trying to do with the >>> research. Open to using something that isn't one drive. That just is where >>> it is stored at the moment >>> >>> Olivia >>> >>> Get Outlook for iOS <https://aka.ms/o0ukef> >>> ------------------------------ >>> *From:* Scott Cain <sc...@sc...> >>> *Sent:* Thursday, October 13, 2022 12:21:13 AM >>> *To:* Rasmussen, Olivia <Oli...@st...> >>> *Cc:* gmo...@li... <gmo...@li...> >>> *Subject:* Re: [Gmod-ajax] URL help >>> >>> You don't often get email from sc...@sc.... Learn why this is >>> important <https://aka.ms/LearnAboutSenderIdentification> >>> Hi Olivia, >>> >>> I wrote a bunch of stuff below, but then went back and reread your >>> email, so maybe I can ask more useful questions. I'll keep the other stuff >>> below a line so you can read it if you want :-) >>> >>> So you have some BAM and BAI files on a Microsoft One Drive and want to >>> use the data on that to load into JBrowse. I've never used one drive. Is it >>> mounted locally so that it "looks like" a local drive, or is it a cloud >>> drive that you have to use some other mechanism to access the data (for >>> example, can you/do you want to access the data via a URL)? If it's a >>> mounted drive and you can load it like it's a local file, I would expect >>> that would work. If you've tried that and it doesn't work, please open the >>> browser's developer tools/javascript console to see if there are any errors >>> and send them to us. >>> >>> If you have to access the data on one drive via a URL, it gets a little >>> trickier. It would make life easier if the data were accessible publicly >>> (meaning you don't need a password or other credential to get it), but that >>> might be possible to work around. Additionally, binary data like BAM have >>> to be accessed via http using a web server that supports range requests, >>> and I have no idea whether one drive does. If you want to give us access to >>> the data, we can try to see if we can sort it out. Again, if you try it and >>> nothing happens, look in the javascript console for error messages. >>> >>> Networking technology aside, do these files load correctly if the files >>> are local on your computer? Things like naming chromosomes the same as your >>> reference sequence frequently trips people up, since "1" is not the same as >>> "chr1" which is also not the same as "Chr1". Just something to look into. >>> >>> Anyway, that's a lot of stuff to get started with. Let us know where to >>> go from here. >>> >>> Scott >>> >>> >>> >>> >>> ------------------------ >>> >>> Maybe you can tell us a little more about what you want to do. As Colin >>> wrote this morning, JBrowse doesn't really "upload" any data at all. If you >>> load local data into the jbrowse instance, it stays on your computer and >>> the web browser just accesses the data locally. If you need to upload >>> something (like so one person can share a view with someone else of data >>> they have on their computer), you have to sort out some way outside of >>> JBrowse to make that happen. If the users are all local to one another, >>> that could be as easy as a shared network drive where the data are placed, >>> or if the users aren't all on the same local network, you could put the >>> data in a cloud resource like AWS S3 (if this is for a student project, you >>> might be able to get a grant from Amazon to supply you with some S3 >>> space). But this is all hand-waving until we really know what you want to >>> do. >>> >>> >>> >>> Scott >>> >>> >>> On Wed, Oct 12, 2022 at 12:14 PM Rasmussen, Olivia < >>> Oli...@st...> wrote: >>> >>> Hello, >>> Yes I am. Sorry I sent both! It’s probably easier via email if that’s >>> alright. I’m just wondering if it’s possible to upload the links directly >>> to jbrowse via a url or if it’s not possible and the data set just needs to >>> be downloaded. I've tried and nothing happens. Uploading the downloaded set >>> from my computer works fine but because the files are large it's not >>> sustainable for the type of project I'm trying to accomplish. >>> >>> Olivia >>> >>> Get Outlook for iOS >>> <https://nam10.safelinks.protection.outlook.com/?url=https%3A%2F%2Faka.ms%2Fo0ukef&data=05%7C01%7COlivia_Rasmussen%40student.uml.edu%7C2ccf3ad164b74bcd265008daacd26477%7C4c25b8a617f746f983f054734ab81fb1%7C0%7C0%7C638012316874605958%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=ObNBohaz0uGMCcWmxsmCahCYVqWT1WUgOaAT5cNlQvQ%3D&reserved=0> >>> ------------------------------ >>> *From:* Scott Cain <sc...@sc...> >>> *Sent:* Wednesday, October 12, 2022 3:06:58 PM >>> *To:* Rasmussen, Olivia <Oli...@st...> >>> *Cc:* gmo...@li... <gmo...@li...> >>> *Subject:* Re: [Gmod-ajax] URL help >>> >>> You don't often get email from sc...@sc.... Learn why this is >>> important <https://aka.ms/LearnAboutSenderIdentification> >>> Hi Olivia, >>> >>> I'm wondering if you are the same person who asked a similar question on >>> gitter. Either is fine with me; you're welcome to have the discussion >>> anywhere you want :-) >>> >>> Scott >>> >>> >>> On Wed, Oct 12, 2022 at 12:05 PM Rasmussen, Olivia < >>> Oli...@st...> wrote: >>> >>> Hello, >>> My name is Olivia and I am a student at Umass Lowell, currently working >>> on a research project which involves teaching high school students how to >>> use Jbrowse. >>> I am wondering gif there is a way to upload data directly from a URL? >>> Currently the data is on a one drive account and I have tried many times to >>> upload the links into the new track box but nothing ever works. We are >>> using BAM and BAI links. Wondering if you have any insight. >>> >>> Thanks, >>> Olivia >>> _______________________________________________ >>> Gmod-ajax mailing list >>> Gmo...@li... >>> https://lists.sourceforge.net/lists/listinfo/gmod-ajax >>> <https://nam10.safelinks.protection.outlook.com/?url=https%3A%2F%2Flists.sourceforge.net%2Flists%2Flistinfo%2Fgmod-ajax&data=05%7C01%7COlivia_Rasmussen%40student.uml.edu%7C2ccf3ad164b74bcd265008daacd26477%7C4c25b8a617f746f983f054734ab81fb1%7C0%7C0%7C638012316874605958%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=qQ%2FBysXzDTQOgjR9l53q8l1FrvrNvB5AtbGCBbV%2BGBQ%3D&reserved=0> >>> >>> >>> >>> -- >>> ------------------------------------------------------------------------ >>> Scott Cain, Ph. D. >>> scott at scottcain dot net >>> GMOD Project Manager (http://gmod.org/ >>> <https://nam10.safelinks.protection.outlook.com/?url=http%3A%2F%2Fgmod.org%2F&data=05%7C01%7COlivia_Rasmussen%40student.uml.edu%7C2ccf3ad164b74bcd265008daacd26477%7C4c25b8a617f746f983f054734ab81fb1%7C0%7C0%7C638012316874605958%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=8U%2F5MVsNSMnlNjFOa6xapvA2%2FYkziLN0va6%2FSz1NCZE%3D&reserved=0>) >>> 216-392-3087 >>> WormBase Developer (http://wormbase.org/ >>> <https://nam10.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwormbase.org%2F&data=05%7C01%7COlivia_Rasmussen%40student.uml.edu%7C2ccf3ad164b74bcd265008daacd26477%7C4c25b8a617f746f983f054734ab81fb1%7C0%7C0%7C638012316874605958%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=gEWlRGTiBO1%2FKdFHmrdBSBATe1iJkYHYnbcyd8x%2BRIk%3D&reserved=0> >>> ) >>> Alliance of Genome Resources Group Leader (http://alliancegenome.org/ >>> <https://nam10.safelinks.protection.outlook.com/?url=http%3A%2F%2Falliancegenome.org%2F&data=05%7C01%7COlivia_Rasmussen%40student.uml.edu%7C2ccf3ad164b74bcd265008daacd26477%7C4c25b8a617f746f983f054734ab81fb1%7C0%7C0%7C638012316874605958%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=MLajm2JStSdqzyGglrCVDfaLxs9M9vJpTWJXhLCyx70%3D&reserved=0> >>> ) >>> VirusSeq Project Manager (https://virusseq-dataportal.ca/ >>> <https://nam10.safelinks.protection.outlook.com/?url=https%3A%2F%2Fvirusseq-dataportal.ca%2F&data=05%7C01%7COlivia_Rasmussen%40student.uml.edu%7C2ccf3ad164b74bcd265008daacd26477%7C4c25b8a617f746f983f054734ab81fb1%7C0%7C0%7C638012316874762656%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=ch%2FVsYa1GkaGMoXsYkZaXEtuT1MsD9klg%2BOYRyeY188%3D&reserved=0> >>> ) >>> Human Cancer Models Initiative Project Manager ( >>> https://hcmi-searchable-catalog.nci.nih.gov/ >>> <https://nam10.safelinks.protection.outlook.com/?url=https%3A%2F%2Fhcmi-searchable-catalog.nci.nih.gov%2F&data=05%7C01%7COlivia_Rasmussen%40student.uml.edu%7C2ccf3ad164b74bcd265008daacd26477%7C4c25b8a617f746f983f054734ab81fb1%7C0%7C0%7C638012316874762656%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=iLXzR21K0WtSljMj04HIcISQezKhJT%2BPlHxCzNUvoyM%3D&reserved=0> >>> ) >>> >>> >>> >>> -- >>> ------------------------------------------------------------------------ >>> Scott Cain, Ph. D. >>> scott at scottcain dot net >>> GMOD Project Manager (http://gmod.org/ >>> <https://nam10.safelinks.protection.outlook.com/?url=http%3A%2F%2Fgmod.org%2F&data=05%7C01%7COlivia_Rasmussen%40student.uml.edu%7C2ccf3ad164b74bcd265008daacd26477%7C4c25b8a617f746f983f054734ab81fb1%7C0%7C0%7C638012316874762656%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=Ef%2FtxFQca4jWYKOCgl2hqUnx8JcY4T66J0aChae6DUs%3D&reserved=0>) >>> 216-392-3087 >>> WormBase Developer (http://wormbase.org/ >>> <https://nam10.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwormbase.org%2F&data=05%7C01%7COlivia_Rasmussen%40student.uml.edu%7C2ccf3ad164b74bcd265008daacd26477%7C4c25b8a617f746f983f054734ab81fb1%7C0%7C0%7C638012316874762656%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=poog6eHte%2FW3uaKJimk7TjuKm13XNHqP79pnDnoohGQ%3D&reserved=0> >>> ) >>> Alliance of Genome Resources Group Leader (http://alliancegenome.org/ >>> <https://nam10.safelinks.protection.outlook.com/?url=http%3A%2F%2Falliancegenome.org%2F&data=05%7C01%7COlivia_Rasmussen%40student.uml.edu%7C2ccf3ad164b74bcd265008daacd26477%7C4c25b8a617f746f983f054734ab81fb1%7C0%7C0%7C638012316874762656%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=fkfJ2bZy0oLsERzABMAzo1VHJ%2Fi6tb5tIiIhxMTKoSo%3D&reserved=0> >>> ) >>> VirusSeq Project Manager (https://virusseq-dataportal.ca/ >>> <https://nam10.safelinks.protection.outlook.com/?url=https%3A%2F%2Fvirusseq-dataportal.ca%2F&data=05%7C01%7COlivia_Rasmussen%40student.uml.edu%7C2ccf3ad164b74bcd265008daacd26477%7C4c25b8a617f746f983f054734ab81fb1%7C0%7C0%7C638012316874762656%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=ch%2FVsYa1GkaGMoXsYkZaXEtuT1MsD9klg%2BOYRyeY188%3D&reserved=0> >>> ) >>> Human Cancer Models Initiative Project Manager ( >>> https://hcmi-searchable-catalog.nci.nih.gov/ >>> <https://nam10.safelinks.protection.outlook.com/?url=https%3A%2F%2Fhcmi-searchable-catalog.nci.nih.gov%2F&data=05%7C01%7COlivia_Rasmussen%40student.uml.edu%7C2ccf3ad164b74bcd265008daacd26477%7C4c25b8a617f746f983f054734ab81fb1%7C0%7C0%7C638012316874762656%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=iLXzR21K0WtSljMj04HIcISQezKhJT%2BPlHxCzNUvoyM%3D&reserved=0> >>> ) >>> >> >> >> -- >> ------------------------------------------------------------------------ >> Scott Cain, Ph. D. scott >> at scottcain dot net >> GMOD Project Manager (http://gmod.org/) >> 216-392-3087 >> WormBase Developer (http://wormbase.org/) >> Alliance of Genome Resources Group Leader (http://alliancegenome.org/) >> VirusSeq Project Manager (https://virusseq-dataportal.ca/) >> Human Cancer Models Initiative Project Manager ( >> https://hcmi-searchable-catalog.nci.nih.gov/) >> > > > -- > ------------------------------------------------------------------------ > Scott Cain, Ph. D. scott > at scottcain dot net > GMOD Project Manager (http://gmod.org/) > 216-392-3087 > WormBase Developer (http://wormbase.org/) > Alliance of Genome Resources Group Leader (http://alliancegenome.org/) > VirusSeq Project Manager (https://virusseq-dataportal.ca/) > Human Cancer Models Initiative Project Manager ( > https://hcmi-searchable-catalog.nci.nih.gov/) > _______________________________________________ > Gmod-ajax mailing list > Gmo...@li... > https://lists.sourceforge.net/lists/listinfo/gmod-ajax > |
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From: Scott C. <sc...@sc...> - 2022-10-19 19:28:55
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The other thing that just occurred to me is relatively low-tech: get a bunch of thumb usb drives (4 or 8 GB ones are pretty cheap) and put the data on them and then just hand them out to your students. On Wed, Oct 19, 2022 at 9:19 AM Scott Cain <sc...@sc...> wrote: > Hi Olivia, > > How much control do you have over the students' learning environment? If > you have access to the machines to set them up before the students use them > and there aren't too many (or you had a good network admin), you could just > place the data files on each computer's hard drive, or if the files are too > big to do that, you could mount the one drive on each of the computers as a > local drive (I googled for directions for how to do that and it looks like > it would probably be doable for Windows and Mac at least). > > If you don't have easy access to the students' machines, then you need to > be able to give them a URL to load data. I have had lots of success with > Amazon Web Services S3 buckets, where I configured the bucket to allow CORS > requests (cross origin resource sharing--required by web servers as a way > to protect against malicious websites from getting dangerous things to your > computer without you knowing it) and then set the data in the S3 bucket as > publicly readable. If you want to go down that route, we can help you with > the details, and I suspect since this is a research project involving > teaching students, you could probably get some S3 storage space from AWS > for free. > > I know that it is also possible to do all of the above (CORS, public read > data, and a URL) with Google Cloud, but I don't know how to do it; I only > know it's possible because I have a track in WormBase's JBrowse that pulls > data from a researcher who put his data in a public Google Cloud space. And > it is possible that you could do all of this with OneDrive, but I don't > know how to do that either. > > The last thing you could do would be to ask the IT staff at UML to set up > a small web server for your project where you could put the data or set one > up yourself if you're allowed by the university; if you wanted to go down > that route, we can help with that too. > > Good luck with your choice, > Scott > > > > > On Wed, Oct 19, 2022 at 5:45 AM Rasmussen, Olivia < > Oli...@st...> wrote: > >> Hello, >> Thanks so much for getting back to me and sorry for the delayed response. >> This is helpful information to know. It seems like the problem is >> definitely that it is not public. I was wondering if there is any sort of >> work around for this? It's okay if not we are just trying to understand the >> best way to approach this based on what we are trying to do with the >> research. Open to using something that isn't one drive. That just is where >> it is stored at the moment >> >> Olivia >> >> Get Outlook for iOS <https://aka.ms/o0ukef> >> ------------------------------ >> *From:* Scott Cain <sc...@sc...> >> *Sent:* Thursday, October 13, 2022 12:21:13 AM >> *To:* Rasmussen, Olivia <Oli...@st...> >> *Cc:* gmo...@li... <gmo...@li...> >> *Subject:* Re: [Gmod-ajax] URL help >> >> You don't often get email from sc...@sc.... Learn why this is >> important <https://aka.ms/LearnAboutSenderIdentification> >> Hi Olivia, >> >> I wrote a bunch of stuff below, but then went back and reread your email, >> so maybe I can ask more useful questions. I'll keep the other stuff below a >> line so you can read it if you want :-) >> >> So you have some BAM and BAI files on a Microsoft One Drive and want to >> use the data on that to load into JBrowse. I've never used one drive. Is it >> mounted locally so that it "looks like" a local drive, or is it a cloud >> drive that you have to use some other mechanism to access the data (for >> example, can you/do you want to access the data via a URL)? If it's a >> mounted drive and you can load it like it's a local file, I would expect >> that would work. If you've tried that and it doesn't work, please open the >> browser's developer tools/javascript console to see if there are any errors >> and send them to us. >> >> If you have to access the data on one drive via a URL, it gets a little >> trickier. It would make life easier if the data were accessible publicly >> (meaning you don't need a password or other credential to get it), but that >> might be possible to work around. Additionally, binary data like BAM have >> to be accessed via http using a web server that supports range requests, >> and I have no idea whether one drive does. If you want to give us access to >> the data, we can try to see if we can sort it out. Again, if you try it and >> nothing happens, look in the javascript console for error messages. >> >> Networking technology aside, do these files load correctly if the files >> are local on your computer? Things like naming chromosomes the same as your >> reference sequence frequently trips people up, since "1" is not the same as >> "chr1" which is also not the same as "Chr1". Just something to look into. >> >> Anyway, that's a lot of stuff to get started with. Let us know where to >> go from here. >> >> Scott >> >> >> >> >> ------------------------ >> >> Maybe you can tell us a little more about what you want to do. As Colin >> wrote this morning, JBrowse doesn't really "upload" any data at all. If you >> load local data into the jbrowse instance, it stays on your computer and >> the web browser just accesses the data locally. If you need to upload >> something (like so one person can share a view with someone else of data >> they have on their computer), you have to sort out some way outside of >> JBrowse to make that happen. If the users are all local to one another, >> that could be as easy as a shared network drive where the data are placed, >> or if the users aren't all on the same local network, you could put the >> data in a cloud resource like AWS S3 (if this is for a student project, you >> might be able to get a grant from Amazon to supply you with some S3 >> space). But this is all hand-waving until we really know what you want to >> do. >> >> >> >> Scott >> >> >> On Wed, Oct 12, 2022 at 12:14 PM Rasmussen, Olivia < >> Oli...@st...> wrote: >> >> Hello, >> Yes I am. Sorry I sent both! It’s probably easier via email if that’s >> alright. I’m just wondering if it’s possible to upload the links directly >> to jbrowse via a url or if it’s not possible and the data set just needs to >> be downloaded. I've tried and nothing happens. Uploading the downloaded set >> from my computer works fine but because the files are large it's not >> sustainable for the type of project I'm trying to accomplish. >> >> Olivia >> >> Get Outlook for iOS >> <https://nam10.safelinks.protection.outlook.com/?url=https%3A%2F%2Faka.ms%2Fo0ukef&data=05%7C01%7COlivia_Rasmussen%40student.uml.edu%7C2ccf3ad164b74bcd265008daacd26477%7C4c25b8a617f746f983f054734ab81fb1%7C0%7C0%7C638012316874605958%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=ObNBohaz0uGMCcWmxsmCahCYVqWT1WUgOaAT5cNlQvQ%3D&reserved=0> >> ------------------------------ >> *From:* Scott Cain <sc...@sc...> >> *Sent:* Wednesday, October 12, 2022 3:06:58 PM >> *To:* Rasmussen, Olivia <Oli...@st...> >> *Cc:* gmo...@li... <gmo...@li...> >> *Subject:* Re: [Gmod-ajax] URL help >> >> You don't often get email from sc...@sc.... Learn why this is >> important <https://aka.ms/LearnAboutSenderIdentification> >> Hi Olivia, >> >> I'm wondering if you are the same person who asked a similar question on >> gitter. Either is fine with me; you're welcome to have the discussion >> anywhere you want :-) >> >> Scott >> >> >> On Wed, Oct 12, 2022 at 12:05 PM Rasmussen, Olivia < >> Oli...@st...> wrote: >> >> Hello, >> My name is Olivia and I am a student at Umass Lowell, currently working >> on a research project which involves teaching high school students how to >> use Jbrowse. >> I am wondering gif there is a way to upload data directly from a URL? >> Currently the data is on a one drive account and I have tried many times to >> upload the links into the new track box but nothing ever works. We are >> using BAM and BAI links. Wondering if you have any insight. >> >> Thanks, >> Olivia >> _______________________________________________ >> Gmod-ajax mailing list >> Gmo...@li... >> https://lists.sourceforge.net/lists/listinfo/gmod-ajax >> <https://nam10.safelinks.protection.outlook.com/?url=https%3A%2F%2Flists.sourceforge.net%2Flists%2Flistinfo%2Fgmod-ajax&data=05%7C01%7COlivia_Rasmussen%40student.uml.edu%7C2ccf3ad164b74bcd265008daacd26477%7C4c25b8a617f746f983f054734ab81fb1%7C0%7C0%7C638012316874605958%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=qQ%2FBysXzDTQOgjR9l53q8l1FrvrNvB5AtbGCBbV%2BGBQ%3D&reserved=0> >> >> >> >> -- >> ------------------------------------------------------------------------ >> Scott Cain, Ph. D. scott >> at scottcain dot net >> GMOD Project Manager (http://gmod.org/ >> <https://nam10.safelinks.protection.outlook.com/?url=http%3A%2F%2Fgmod.org%2F&data=05%7C01%7COlivia_Rasmussen%40student.uml.edu%7C2ccf3ad164b74bcd265008daacd26477%7C4c25b8a617f746f983f054734ab81fb1%7C0%7C0%7C638012316874605958%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=8U%2F5MVsNSMnlNjFOa6xapvA2%2FYkziLN0va6%2FSz1NCZE%3D&reserved=0>) >> 216-392-3087 >> WormBase Developer (http://wormbase.org/ >> <https://nam10.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwormbase.org%2F&data=05%7C01%7COlivia_Rasmussen%40student.uml.edu%7C2ccf3ad164b74bcd265008daacd26477%7C4c25b8a617f746f983f054734ab81fb1%7C0%7C0%7C638012316874605958%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=gEWlRGTiBO1%2FKdFHmrdBSBATe1iJkYHYnbcyd8x%2BRIk%3D&reserved=0> >> ) >> Alliance of Genome Resources Group Leader (http://alliancegenome.org/ >> <https://nam10.safelinks.protection.outlook.com/?url=http%3A%2F%2Falliancegenome.org%2F&data=05%7C01%7COlivia_Rasmussen%40student.uml.edu%7C2ccf3ad164b74bcd265008daacd26477%7C4c25b8a617f746f983f054734ab81fb1%7C0%7C0%7C638012316874605958%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=MLajm2JStSdqzyGglrCVDfaLxs9M9vJpTWJXhLCyx70%3D&reserved=0> >> ) >> VirusSeq Project Manager (https://virusseq-dataportal.ca/ >> <https://nam10.safelinks.protection.outlook.com/?url=https%3A%2F%2Fvirusseq-dataportal.ca%2F&data=05%7C01%7COlivia_Rasmussen%40student.uml.edu%7C2ccf3ad164b74bcd265008daacd26477%7C4c25b8a617f746f983f054734ab81fb1%7C0%7C0%7C638012316874762656%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=ch%2FVsYa1GkaGMoXsYkZaXEtuT1MsD9klg%2BOYRyeY188%3D&reserved=0> >> ) >> Human Cancer Models Initiative Project Manager ( >> https://hcmi-searchable-catalog.nci.nih.gov/ >> <https://nam10.safelinks.protection.outlook.com/?url=https%3A%2F%2Fhcmi-searchable-catalog.nci.nih.gov%2F&data=05%7C01%7COlivia_Rasmussen%40student.uml.edu%7C2ccf3ad164b74bcd265008daacd26477%7C4c25b8a617f746f983f054734ab81fb1%7C0%7C0%7C638012316874762656%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=iLXzR21K0WtSljMj04HIcISQezKhJT%2BPlHxCzNUvoyM%3D&reserved=0> >> ) >> >> >> >> -- >> ------------------------------------------------------------------------ >> Scott Cain, Ph. D. scott >> at scottcain dot net >> GMOD Project Manager (http://gmod.org/ >> <https://nam10.safelinks.protection.outlook.com/?url=http%3A%2F%2Fgmod.org%2F&data=05%7C01%7COlivia_Rasmussen%40student.uml.edu%7C2ccf3ad164b74bcd265008daacd26477%7C4c25b8a617f746f983f054734ab81fb1%7C0%7C0%7C638012316874762656%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=Ef%2FtxFQca4jWYKOCgl2hqUnx8JcY4T66J0aChae6DUs%3D&reserved=0>) >> 216-392-3087 >> WormBase Developer (http://wormbase.org/ >> <https://nam10.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwormbase.org%2F&data=05%7C01%7COlivia_Rasmussen%40student.uml.edu%7C2ccf3ad164b74bcd265008daacd26477%7C4c25b8a617f746f983f054734ab81fb1%7C0%7C0%7C638012316874762656%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=poog6eHte%2FW3uaKJimk7TjuKm13XNHqP79pnDnoohGQ%3D&reserved=0> >> ) >> Alliance of Genome Resources Group Leader (http://alliancegenome.org/ >> <https://nam10.safelinks.protection.outlook.com/?url=http%3A%2F%2Falliancegenome.org%2F&data=05%7C01%7COlivia_Rasmussen%40student.uml.edu%7C2ccf3ad164b74bcd265008daacd26477%7C4c25b8a617f746f983f054734ab81fb1%7C0%7C0%7C638012316874762656%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=fkfJ2bZy0oLsERzABMAzo1VHJ%2Fi6tb5tIiIhxMTKoSo%3D&reserved=0> >> ) >> VirusSeq Project Manager (https://virusseq-dataportal.ca/ >> <https://nam10.safelinks.protection.outlook.com/?url=https%3A%2F%2Fvirusseq-dataportal.ca%2F&data=05%7C01%7COlivia_Rasmussen%40student.uml.edu%7C2ccf3ad164b74bcd265008daacd26477%7C4c25b8a617f746f983f054734ab81fb1%7C0%7C0%7C638012316874762656%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=ch%2FVsYa1GkaGMoXsYkZaXEtuT1MsD9klg%2BOYRyeY188%3D&reserved=0> >> ) >> Human Cancer Models Initiative Project Manager ( >> https://hcmi-searchable-catalog.nci.nih.gov/ >> <https://nam10.safelinks.protection.outlook.com/?url=https%3A%2F%2Fhcmi-searchable-catalog.nci.nih.gov%2F&data=05%7C01%7COlivia_Rasmussen%40student.uml.edu%7C2ccf3ad164b74bcd265008daacd26477%7C4c25b8a617f746f983f054734ab81fb1%7C0%7C0%7C638012316874762656%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=iLXzR21K0WtSljMj04HIcISQezKhJT%2BPlHxCzNUvoyM%3D&reserved=0> >> ) >> > > > -- > ------------------------------------------------------------------------ > Scott Cain, Ph. D. scott > at scottcain dot net > GMOD Project Manager (http://gmod.org/) > 216-392-3087 > WormBase Developer (http://wormbase.org/) > Alliance of Genome Resources Group Leader (http://alliancegenome.org/) > VirusSeq Project Manager (https://virusseq-dataportal.ca/) > Human Cancer Models Initiative Project Manager ( > https://hcmi-searchable-catalog.nci.nih.gov/) > -- ------------------------------------------------------------------------ Scott Cain, Ph. D. scott at scottcain dot net GMOD Project Manager (http://gmod.org/) 216-392-3087 WormBase Developer (http://wormbase.org/) Alliance of Genome Resources Group Leader (http://alliancegenome.org/) VirusSeq Project Manager (https://virusseq-dataportal.ca/) Human Cancer Models Initiative Project Manager ( https://hcmi-searchable-catalog.nci.nih.gov/) |
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From: Scott C. <sc...@sc...> - 2022-10-19 16:45:48
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Hi Olivia, How much control do you have over the students' learning environment? If you have access to the machines to set them up before the students use them and there aren't too many (or you had a good network admin), you could just place the data files on each computer's hard drive, or if the files are too big to do that, you could mount the one drive on each of the computers as a local drive (I googled for directions for how to do that and it looks like it would probably be doable for Windows and Mac at least). If you don't have easy access to the students' machines, then you need to be able to give them a URL to load data. I have had lots of success with Amazon Web Services S3 buckets, where I configured the bucket to allow CORS requests (cross origin resource sharing--required by web servers as a way to protect against malicious websites from getting dangerous things to your computer without you knowing it) and then set the data in the S3 bucket as publicly readable. If you want to go down that route, we can help you with the details, and I suspect since this is a research project involving teaching students, you could probably get some S3 storage space from AWS for free. I know that it is also possible to do all of the above (CORS, public read data, and a URL) with Google Cloud, but I don't know how to do it; I only know it's possible because I have a track in WormBase's JBrowse that pulls data from a researcher who put his data in a public Google Cloud space. And it is possible that you could do all of this with OneDrive, but I don't know how to do that either. The last thing you could do would be to ask the IT staff at UML to set up a small web server for your project where you could put the data or set one up yourself if you're allowed by the university; if you wanted to go down that route, we can help with that too. Good luck with your choice, Scott On Wed, Oct 19, 2022 at 5:45 AM Rasmussen, Olivia < Oli...@st...> wrote: > Hello, > Thanks so much for getting back to me and sorry for the delayed response. > This is helpful information to know. It seems like the problem is > definitely that it is not public. I was wondering if there is any sort of > work around for this? It's okay if not we are just trying to understand the > best way to approach this based on what we are trying to do with the > research. Open to using something that isn't one drive. That just is where > it is stored at the moment > > Olivia > > Get Outlook for iOS <https://aka.ms/o0ukef> > ------------------------------ > *From:* Scott Cain <sc...@sc...> > *Sent:* Thursday, October 13, 2022 12:21:13 AM > *To:* Rasmussen, Olivia <Oli...@st...> > *Cc:* gmo...@li... <gmo...@li...> > *Subject:* Re: [Gmod-ajax] URL help > > You don't often get email from sc...@sc.... Learn why this is > important <https://aka.ms/LearnAboutSenderIdentification> > Hi Olivia, > > I wrote a bunch of stuff below, but then went back and reread your email, > so maybe I can ask more useful questions. I'll keep the other stuff below a > line so you can read it if you want :-) > > So you have some BAM and BAI files on a Microsoft One Drive and want to > use the data on that to load into JBrowse. I've never used one drive. Is it > mounted locally so that it "looks like" a local drive, or is it a cloud > drive that you have to use some other mechanism to access the data (for > example, can you/do you want to access the data via a URL)? If it's a > mounted drive and you can load it like it's a local file, I would expect > that would work. If you've tried that and it doesn't work, please open the > browser's developer tools/javascript console to see if there are any errors > and send them to us. > > If you have to access the data on one drive via a URL, it gets a little > trickier. It would make life easier if the data were accessible publicly > (meaning you don't need a password or other credential to get it), but that > might be possible to work around. Additionally, binary data like BAM have > to be accessed via http using a web server that supports range requests, > and I have no idea whether one drive does. If you want to give us access to > the data, we can try to see if we can sort it out. Again, if you try it and > nothing happens, look in the javascript console for error messages. > > Networking technology aside, do these files load correctly if the files > are local on your computer? Things like naming chromosomes the same as your > reference sequence frequently trips people up, since "1" is not the same as > "chr1" which is also not the same as "Chr1". Just something to look into. > > Anyway, that's a lot of stuff to get started with. Let us know where to > go from here. > > Scott > > > > > ------------------------ > > Maybe you can tell us a little more about what you want to do. As Colin > wrote this morning, JBrowse doesn't really "upload" any data at all. If you > load local data into the jbrowse instance, it stays on your computer and > the web browser just accesses the data locally. If you need to upload > something (like so one person can share a view with someone else of data > they have on their computer), you have to sort out some way outside of > JBrowse to make that happen. If the users are all local to one another, > that could be as easy as a shared network drive where the data are placed, > or if the users aren't all on the same local network, you could put the > data in a cloud resource like AWS S3 (if this is for a student project, you > might be able to get a grant from Amazon to supply you with some S3 > space). But this is all hand-waving until we really know what you want to > do. > > > > Scott > > > On Wed, Oct 12, 2022 at 12:14 PM Rasmussen, Olivia < > Oli...@st...> wrote: > > Hello, > Yes I am. Sorry I sent both! It’s probably easier via email if that’s > alright. I’m just wondering if it’s possible to upload the links directly > to jbrowse via a url or if it’s not possible and the data set just needs to > be downloaded. I've tried and nothing happens. Uploading the downloaded set > from my computer works fine but because the files are large it's not > sustainable for the type of project I'm trying to accomplish. > > Olivia > > Get Outlook for iOS > <https://nam10.safelinks.protection.outlook.com/?url=https%3A%2F%2Faka.ms%2Fo0ukef&data=05%7C01%7COlivia_Rasmussen%40student.uml.edu%7C2ccf3ad164b74bcd265008daacd26477%7C4c25b8a617f746f983f054734ab81fb1%7C0%7C0%7C638012316874605958%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=ObNBohaz0uGMCcWmxsmCahCYVqWT1WUgOaAT5cNlQvQ%3D&reserved=0> > ------------------------------ > *From:* Scott Cain <sc...@sc...> > *Sent:* Wednesday, October 12, 2022 3:06:58 PM > *To:* Rasmussen, Olivia <Oli...@st...> > *Cc:* gmo...@li... <gmo...@li...> > *Subject:* Re: [Gmod-ajax] URL help > > You don't often get email from sc...@sc.... Learn why this is > important <https://aka.ms/LearnAboutSenderIdentification> > Hi Olivia, > > I'm wondering if you are the same person who asked a similar question on > gitter. Either is fine with me; you're welcome to have the discussion > anywhere you want :-) > > Scott > > > On Wed, Oct 12, 2022 at 12:05 PM Rasmussen, Olivia < > Oli...@st...> wrote: > > Hello, > My name is Olivia and I am a student at Umass Lowell, currently working on > a research project which involves teaching high school students how to use > Jbrowse. > I am wondering gif there is a way to upload data directly from a URL? > Currently the data is on a one drive account and I have tried many times to > upload the links into the new track box but nothing ever works. We are > using BAM and BAI links. Wondering if you have any insight. > > Thanks, > Olivia > _______________________________________________ > Gmod-ajax mailing list > Gmo...@li... > https://lists.sourceforge.net/lists/listinfo/gmod-ajax > <https://nam10.safelinks.protection.outlook.com/?url=https%3A%2F%2Flists.sourceforge.net%2Flists%2Flistinfo%2Fgmod-ajax&data=05%7C01%7COlivia_Rasmussen%40student.uml.edu%7C2ccf3ad164b74bcd265008daacd26477%7C4c25b8a617f746f983f054734ab81fb1%7C0%7C0%7C638012316874605958%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=qQ%2FBysXzDTQOgjR9l53q8l1FrvrNvB5AtbGCBbV%2BGBQ%3D&reserved=0> > > > > -- > ------------------------------------------------------------------------ > Scott Cain, Ph. D. scott > at scottcain dot net > GMOD Project Manager (http://gmod.org/ > <https://nam10.safelinks.protection.outlook.com/?url=http%3A%2F%2Fgmod.org%2F&data=05%7C01%7COlivia_Rasmussen%40student.uml.edu%7C2ccf3ad164b74bcd265008daacd26477%7C4c25b8a617f746f983f054734ab81fb1%7C0%7C0%7C638012316874605958%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=8U%2F5MVsNSMnlNjFOa6xapvA2%2FYkziLN0va6%2FSz1NCZE%3D&reserved=0>) > 216-392-3087 > WormBase Developer (http://wormbase.org/ > <https://nam10.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwormbase.org%2F&data=05%7C01%7COlivia_Rasmussen%40student.uml.edu%7C2ccf3ad164b74bcd265008daacd26477%7C4c25b8a617f746f983f054734ab81fb1%7C0%7C0%7C638012316874605958%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=gEWlRGTiBO1%2FKdFHmrdBSBATe1iJkYHYnbcyd8x%2BRIk%3D&reserved=0> > ) > Alliance of Genome Resources Group Leader (http://alliancegenome.org/ > <https://nam10.safelinks.protection.outlook.com/?url=http%3A%2F%2Falliancegenome.org%2F&data=05%7C01%7COlivia_Rasmussen%40student.uml.edu%7C2ccf3ad164b74bcd265008daacd26477%7C4c25b8a617f746f983f054734ab81fb1%7C0%7C0%7C638012316874605958%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=MLajm2JStSdqzyGglrCVDfaLxs9M9vJpTWJXhLCyx70%3D&reserved=0> > ) > VirusSeq Project Manager (https://virusseq-dataportal.ca/ > <https://nam10.safelinks.protection.outlook.com/?url=https%3A%2F%2Fvirusseq-dataportal.ca%2F&data=05%7C01%7COlivia_Rasmussen%40student.uml.edu%7C2ccf3ad164b74bcd265008daacd26477%7C4c25b8a617f746f983f054734ab81fb1%7C0%7C0%7C638012316874762656%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=ch%2FVsYa1GkaGMoXsYkZaXEtuT1MsD9klg%2BOYRyeY188%3D&reserved=0> > ) > Human Cancer Models Initiative Project Manager ( > https://hcmi-searchable-catalog.nci.nih.gov/ > <https://nam10.safelinks.protection.outlook.com/?url=https%3A%2F%2Fhcmi-searchable-catalog.nci.nih.gov%2F&data=05%7C01%7COlivia_Rasmussen%40student.uml.edu%7C2ccf3ad164b74bcd265008daacd26477%7C4c25b8a617f746f983f054734ab81fb1%7C0%7C0%7C638012316874762656%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=iLXzR21K0WtSljMj04HIcISQezKhJT%2BPlHxCzNUvoyM%3D&reserved=0> > ) > > > > -- > ------------------------------------------------------------------------ > Scott Cain, Ph. D. scott > at scottcain dot net > GMOD Project Manager (http://gmod.org/ > <https://nam10.safelinks.protection.outlook.com/?url=http%3A%2F%2Fgmod.org%2F&data=05%7C01%7COlivia_Rasmussen%40student.uml.edu%7C2ccf3ad164b74bcd265008daacd26477%7C4c25b8a617f746f983f054734ab81fb1%7C0%7C0%7C638012316874762656%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=Ef%2FtxFQca4jWYKOCgl2hqUnx8JcY4T66J0aChae6DUs%3D&reserved=0>) > 216-392-3087 > WormBase Developer (http://wormbase.org/ > <https://nam10.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwormbase.org%2F&data=05%7C01%7COlivia_Rasmussen%40student.uml.edu%7C2ccf3ad164b74bcd265008daacd26477%7C4c25b8a617f746f983f054734ab81fb1%7C0%7C0%7C638012316874762656%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=poog6eHte%2FW3uaKJimk7TjuKm13XNHqP79pnDnoohGQ%3D&reserved=0> > ) > Alliance of Genome Resources Group Leader (http://alliancegenome.org/ > <https://nam10.safelinks.protection.outlook.com/?url=http%3A%2F%2Falliancegenome.org%2F&data=05%7C01%7COlivia_Rasmussen%40student.uml.edu%7C2ccf3ad164b74bcd265008daacd26477%7C4c25b8a617f746f983f054734ab81fb1%7C0%7C0%7C638012316874762656%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=fkfJ2bZy0oLsERzABMAzo1VHJ%2Fi6tb5tIiIhxMTKoSo%3D&reserved=0> > ) > VirusSeq Project Manager (https://virusseq-dataportal.ca/ > <https://nam10.safelinks.protection.outlook.com/?url=https%3A%2F%2Fvirusseq-dataportal.ca%2F&data=05%7C01%7COlivia_Rasmussen%40student.uml.edu%7C2ccf3ad164b74bcd265008daacd26477%7C4c25b8a617f746f983f054734ab81fb1%7C0%7C0%7C638012316874762656%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=ch%2FVsYa1GkaGMoXsYkZaXEtuT1MsD9klg%2BOYRyeY188%3D&reserved=0> > ) > Human Cancer Models Initiative Project Manager ( > https://hcmi-searchable-catalog.nci.nih.gov/ > <https://nam10.safelinks.protection.outlook.com/?url=https%3A%2F%2Fhcmi-searchable-catalog.nci.nih.gov%2F&data=05%7C01%7COlivia_Rasmussen%40student.uml.edu%7C2ccf3ad164b74bcd265008daacd26477%7C4c25b8a617f746f983f054734ab81fb1%7C0%7C0%7C638012316874762656%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=iLXzR21K0WtSljMj04HIcISQezKhJT%2BPlHxCzNUvoyM%3D&reserved=0> > ) > -- ------------------------------------------------------------------------ Scott Cain, Ph. D. scott at scottcain dot net GMOD Project Manager (http://gmod.org/) 216-392-3087 WormBase Developer (http://wormbase.org/) Alliance of Genome Resources Group Leader (http://alliancegenome.org/) VirusSeq Project Manager (https://virusseq-dataportal.ca/) Human Cancer Models Initiative Project Manager ( https://hcmi-searchable-catalog.nci.nih.gov/) |
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From: Rasmussen, O. <Oli...@st...> - 2022-10-19 16:20:50
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Hello, Thanks so much for getting back to me and sorry for the delayed response. This is helpful information to know. It seems like the problem is definitely that it is not public. I was wondering if there is any sort of work around for this? It's okay if not we are just trying to understand the best way to approach this based on what we are trying to do with the research. Open to using something that isn't one drive. That just is where it is stored at the moment Olivia Get Outlook for iOS<https://aka.ms/o0ukef> ________________________________ From: Scott Cain <sc...@sc...> Sent: Thursday, October 13, 2022 12:21:13 AM To: Rasmussen, Olivia <Oli...@st...> Cc: gmo...@li... <gmo...@li...> Subject: Re: [Gmod-ajax] URL help You don't often get email from sc...@sc.... Learn why this is important<https://aka.ms/LearnAboutSenderIdentification> Hi Olivia, I wrote a bunch of stuff below, but then went back and reread your email, so maybe I can ask more useful questions. I'll keep the other stuff below a line so you can read it if you want :-) So you have some BAM and BAI files on a Microsoft One Drive and want to use the data on that to load into JBrowse. I've never used one drive. Is it mounted locally so that it "looks like" a local drive, or is it a cloud drive that you have to use some other mechanism to access the data (for example, can you/do you want to access the data via a URL)? If it's a mounted drive and you can load it like it's a local file, I would expect that would work. If you've tried that and it doesn't work, please open the browser's developer tools/javascript console to see if there are any errors and send them to us. If you have to access the data on one drive via a URL, it gets a little trickier. It would make life easier if the data were accessible publicly (meaning you don't need a password or other credential to get it), but that might be possible to work around. Additionally, binary data like BAM have to be accessed via http using a web server that supports range requests, and I have no idea whether one drive does. If you want to give us access to the data, we can try to see if we can sort it out. Again, if you try it and nothing happens, look in the javascript console for error messages. Networking technology aside, do these files load correctly if the files are local on your computer? Things like naming chromosomes the same as your reference sequence frequently trips people up, since "1" is not the same as "chr1" which is also not the same as "Chr1". Just something to look into. Anyway, that's a lot of stuff to get started with. Let us know where to go from here. Scott ------------------------ Maybe you can tell us a little more about what you want to do. As Colin wrote this morning, JBrowse doesn't really "upload" any data at all. If you load local data into the jbrowse instance, it stays on your computer and the web browser just accesses the data locally. If you need to upload something (like so one person can share a view with someone else of data they have on their computer), you have to sort out some way outside of JBrowse to make that happen. If the users are all local to one another, that could be as easy as a shared network drive where the data are placed, or if the users aren't all on the same local network, you could put the data in a cloud resource like AWS S3 (if this is for a student project, you might be able to get a grant from Amazon to supply you with some S3 space). But this is all hand-waving until we really know what you want to do. Scott On Wed, Oct 12, 2022 at 12:14 PM Rasmussen, Olivia <Oli...@st...<mailto:Oli...@st...>> wrote: Hello, Yes I am. Sorry I sent both! It’s probably easier via email if that’s alright. I’m just wondering if it’s possible to upload the links directly to jbrowse via a url or if it’s not possible and the data set just needs to be downloaded. I've tried and nothing happens. Uploading the downloaded set from my computer works fine but because the files are large it's not sustainable for the type of project I'm trying to accomplish. Olivia Get Outlook for iOS<https://nam10.safelinks.protection.outlook.com/?url=https%3A%2F%2Faka.ms%2Fo0ukef&data=05%7C01%7COlivia_Rasmussen%40student.uml.edu%7C2ccf3ad164b74bcd265008daacd26477%7C4c25b8a617f746f983f054734ab81fb1%7C0%7C0%7C638012316874605958%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=ObNBohaz0uGMCcWmxsmCahCYVqWT1WUgOaAT5cNlQvQ%3D&reserved=0> ________________________________ From: Scott Cain <sc...@sc...<mailto:sc...@sc...>> Sent: Wednesday, October 12, 2022 3:06:58 PM To: Rasmussen, Olivia <Oli...@st...<mailto:Oli...@st...>> Cc: gmo...@li...<mailto:gmo...@li...> <gmo...@li...<mailto:gmo...@li...>> Subject: Re: [Gmod-ajax] URL help You don't often get email from sc...@sc...<mailto:sc...@sc...>. Learn why this is important<https://aka.ms/LearnAboutSenderIdentification> Hi Olivia, I'm wondering if you are the same person who asked a similar question on gitter. Either is fine with me; you're welcome to have the discussion anywhere you want :-) Scott On Wed, Oct 12, 2022 at 12:05 PM Rasmussen, Olivia <Oli...@st...<mailto:Oli...@st...>> wrote: Hello, My name is Olivia and I am a student at Umass Lowell, currently working on a research project which involves teaching high school students how to use Jbrowse. I am wondering gif there is a way to upload data directly from a URL? Currently the data is on a one drive account and I have tried many times to upload the links into the new track box but nothing ever works. We are using BAM and BAI links. Wondering if you have any insight. Thanks, Olivia _______________________________________________ Gmod-ajax mailing list Gmo...@li...<mailto:Gmo...@li...> https://lists.sourceforge.net/lists/listinfo/gmod-ajax<https://nam10.safelinks.protection.outlook.com/?url=https%3A%2F%2Flists.sourceforge.net%2Flists%2Flistinfo%2Fgmod-ajax&data=05%7C01%7COlivia_Rasmussen%40student.uml.edu%7C2ccf3ad164b74bcd265008daacd26477%7C4c25b8a617f746f983f054734ab81fb1%7C0%7C0%7C638012316874605958%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=qQ%2FBysXzDTQOgjR9l53q8l1FrvrNvB5AtbGCBbV%2BGBQ%3D&reserved=0> -- ------------------------------------------------------------------------ Scott Cain, Ph. D. scott at scottcain dot net GMOD Project Manager (http://gmod.org/<https://nam10.safelinks.protection.outlook.com/?url=http%3A%2F%2Fgmod.org%2F&data=05%7C01%7COlivia_Rasmussen%40student.uml.edu%7C2ccf3ad164b74bcd265008daacd26477%7C4c25b8a617f746f983f054734ab81fb1%7C0%7C0%7C638012316874605958%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=8U%2F5MVsNSMnlNjFOa6xapvA2%2FYkziLN0va6%2FSz1NCZE%3D&reserved=0>) 216-392-3087 WormBase Developer (http://wormbase.org/<https://nam10.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwormbase.org%2F&data=05%7C01%7COlivia_Rasmussen%40student.uml.edu%7C2ccf3ad164b74bcd265008daacd26477%7C4c25b8a617f746f983f054734ab81fb1%7C0%7C0%7C638012316874605958%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=gEWlRGTiBO1%2FKdFHmrdBSBATe1iJkYHYnbcyd8x%2BRIk%3D&reserved=0>) Alliance of Genome Resources Group Leader (http://alliancegenome.org/<https://nam10.safelinks.protection.outlook.com/?url=http%3A%2F%2Falliancegenome.org%2F&data=05%7C01%7COlivia_Rasmussen%40student.uml.edu%7C2ccf3ad164b74bcd265008daacd26477%7C4c25b8a617f746f983f054734ab81fb1%7C0%7C0%7C638012316874605958%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=MLajm2JStSdqzyGglrCVDfaLxs9M9vJpTWJXhLCyx70%3D&reserved=0>) VirusSeq Project Manager (https://virusseq-dataportal.ca/<https://nam10.safelinks.protection.outlook.com/?url=https%3A%2F%2Fvirusseq-dataportal.ca%2F&data=05%7C01%7COlivia_Rasmussen%40student.uml.edu%7C2ccf3ad164b74bcd265008daacd26477%7C4c25b8a617f746f983f054734ab81fb1%7C0%7C0%7C638012316874762656%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=ch%2FVsYa1GkaGMoXsYkZaXEtuT1MsD9klg%2BOYRyeY188%3D&reserved=0>) Human Cancer Models Initiative Project Manager (https://hcmi-searchable-catalog.nci.nih.gov/<https://nam10.safelinks.protection.outlook.com/?url=https%3A%2F%2Fhcmi-searchable-catalog.nci.nih.gov%2F&data=05%7C01%7COlivia_Rasmussen%40student.uml.edu%7C2ccf3ad164b74bcd265008daacd26477%7C4c25b8a617f746f983f054734ab81fb1%7C0%7C0%7C638012316874762656%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=iLXzR21K0WtSljMj04HIcISQezKhJT%2BPlHxCzNUvoyM%3D&reserved=0>) -- ------------------------------------------------------------------------ Scott Cain, Ph. D. scott at scottcain dot net GMOD Project Manager (http://gmod.org/<https://nam10.safelinks.protection.outlook.com/?url=http%3A%2F%2Fgmod.org%2F&data=05%7C01%7COlivia_Rasmussen%40student.uml.edu%7C2ccf3ad164b74bcd265008daacd26477%7C4c25b8a617f746f983f054734ab81fb1%7C0%7C0%7C638012316874762656%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=Ef%2FtxFQca4jWYKOCgl2hqUnx8JcY4T66J0aChae6DUs%3D&reserved=0>) 216-392-3087 WormBase Developer (http://wormbase.org/<https://nam10.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwormbase.org%2F&data=05%7C01%7COlivia_Rasmussen%40student.uml.edu%7C2ccf3ad164b74bcd265008daacd26477%7C4c25b8a617f746f983f054734ab81fb1%7C0%7C0%7C638012316874762656%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=poog6eHte%2FW3uaKJimk7TjuKm13XNHqP79pnDnoohGQ%3D&reserved=0>) Alliance of Genome Resources Group Leader (http://alliancegenome.org/<https://nam10.safelinks.protection.outlook.com/?url=http%3A%2F%2Falliancegenome.org%2F&data=05%7C01%7COlivia_Rasmussen%40student.uml.edu%7C2ccf3ad164b74bcd265008daacd26477%7C4c25b8a617f746f983f054734ab81fb1%7C0%7C0%7C638012316874762656%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=fkfJ2bZy0oLsERzABMAzo1VHJ%2Fi6tb5tIiIhxMTKoSo%3D&reserved=0>) VirusSeq Project Manager (https://virusseq-dataportal.ca/<https://nam10.safelinks.protection.outlook.com/?url=https%3A%2F%2Fvirusseq-dataportal.ca%2F&data=05%7C01%7COlivia_Rasmussen%40student.uml.edu%7C2ccf3ad164b74bcd265008daacd26477%7C4c25b8a617f746f983f054734ab81fb1%7C0%7C0%7C638012316874762656%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=ch%2FVsYa1GkaGMoXsYkZaXEtuT1MsD9klg%2BOYRyeY188%3D&reserved=0>) Human Cancer Models Initiative Project Manager (https://hcmi-searchable-catalog.nci.nih.gov/<https://nam10.safelinks.protection.outlook.com/?url=https%3A%2F%2Fhcmi-searchable-catalog.nci.nih.gov%2F&data=05%7C01%7COlivia_Rasmussen%40student.uml.edu%7C2ccf3ad164b74bcd265008daacd26477%7C4c25b8a617f746f983f054734ab81fb1%7C0%7C0%7C638012316874762656%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=iLXzR21K0WtSljMj04HIcISQezKhJT%2BPlHxCzNUvoyM%3D&reserved=0>) |
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From: Scott C. <sc...@sc...> - 2022-10-13 04:21:39
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Hi Olivia, I wrote a bunch of stuff below, but then went back and reread your email, so maybe I can ask more useful questions. I'll keep the other stuff below a line so you can read it if you want :-) So you have some BAM and BAI files on a Microsoft One Drive and want to use the data on that to load into JBrowse. I've never used one drive. Is it mounted locally so that it "looks like" a local drive, or is it a cloud drive that you have to use some other mechanism to access the data (for example, can you/do you want to access the data via a URL)? If it's a mounted drive and you can load it like it's a local file, I would expect that would work. If you've tried that and it doesn't work, please open the browser's developer tools/javascript console to see if there are any errors and send them to us. If you have to access the data on one drive via a URL, it gets a little trickier. It would make life easier if the data were accessible publicly (meaning you don't need a password or other credential to get it), but that might be possible to work around. Additionally, binary data like BAM have to be accessed via http using a web server that supports range requests, and I have no idea whether one drive does. If you want to give us access to the data, we can try to see if we can sort it out. Again, if you try it and nothing happens, look in the javascript console for error messages. Networking technology aside, do these files load correctly if the files are local on your computer? Things like naming chromosomes the same as your reference sequence frequently trips people up, since "1" is not the same as "chr1" which is also not the same as "Chr1". Just something to look into. Anyway, that's a lot of stuff to get started with. Let us know where to go from here. Scott ------------------------ Maybe you can tell us a little more about what you want to do. As Colin wrote this morning, JBrowse doesn't really "upload" any data at all. If you load local data into the jbrowse instance, it stays on your computer and the web browser just accesses the data locally. If you need to upload something (like so one person can share a view with someone else of data they have on their computer), you have to sort out some way outside of JBrowse to make that happen. If the users are all local to one another, that could be as easy as a shared network drive where the data are placed, or if the users aren't all on the same local network, you could put the data in a cloud resource like AWS S3 (if this is for a student project, you might be able to get a grant from Amazon to supply you with some S3 space). But this is all hand-waving until we really know what you want to do. Scott On Wed, Oct 12, 2022 at 12:14 PM Rasmussen, Olivia < Oli...@st...> wrote: > Hello, > Yes I am. Sorry I sent both! It’s probably easier via email if that’s > alright. I’m just wondering if it’s possible to upload the links directly > to jbrowse via a url or if it’s not possible and the data set just needs to > be downloaded. I've tried and nothing happens. Uploading the downloaded set > from my computer works fine but because the files are large it's not > sustainable for the type of project I'm trying to accomplish. > > Olivia > > Get Outlook for iOS <https://aka.ms/o0ukef> > ------------------------------ > *From:* Scott Cain <sc...@sc...> > *Sent:* Wednesday, October 12, 2022 3:06:58 PM > *To:* Rasmussen, Olivia <Oli...@st...> > *Cc:* gmo...@li... <gmo...@li...> > *Subject:* Re: [Gmod-ajax] URL help > > You don't often get email from sc...@sc.... Learn why this is > important <https://aka.ms/LearnAboutSenderIdentification> > Hi Olivia, > > I'm wondering if you are the same person who asked a similar question on > gitter. Either is fine with me; you're welcome to have the discussion > anywhere you want :-) > > Scott > > > On Wed, Oct 12, 2022 at 12:05 PM Rasmussen, Olivia < > Oli...@st...> wrote: > > Hello, > My name is Olivia and I am a student at Umass Lowell, currently working on > a research project which involves teaching high school students how to use > Jbrowse. > I am wondering gif there is a way to upload data directly from a URL? > Currently the data is on a one drive account and I have tried many times to > upload the links into the new track box but nothing ever works. We are > using BAM and BAI links. Wondering if you have any insight. > > Thanks, > Olivia > _______________________________________________ > Gmod-ajax mailing list > Gmo...@li... > https://lists.sourceforge.net/lists/listinfo/gmod-ajax > <https://nam10.safelinks.protection.outlook.com/?url=https%3A%2F%2Flists.sourceforge.net%2Flists%2Flistinfo%2Fgmod-ajax&data=05%7C01%7COlivia_Rasmussen%40student.uml.edu%7C35ea5e2a7763468bdceb08daac84f785%7C4c25b8a617f746f983f054734ab81fb1%7C0%7C0%7C638011984335030060%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=hPRlitPKF41f6x7ZD9n21TtiIIjGQeXhEaxyn%2BPC8%2Bw%3D&reserved=0> > > > > -- > ------------------------------------------------------------------------ > Scott Cain, Ph. D. scott > at scottcain dot net > GMOD Project Manager (http://gmod.org/ > <https://nam10.safelinks.protection.outlook.com/?url=http%3A%2F%2Fgmod.org%2F&data=05%7C01%7COlivia_Rasmussen%40student.uml.edu%7C35ea5e2a7763468bdceb08daac84f785%7C4c25b8a617f746f983f054734ab81fb1%7C0%7C0%7C638011984335186283%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=8qdJOemrYrxjj2LTDuxdowLsqCgyHNf%2FSlWs9xus2uM%3D&reserved=0>) > 216-392-3087 > WormBase Developer (http://wormbase.org/ > <https://nam10.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwormbase.org%2F&data=05%7C01%7COlivia_Rasmussen%40student.uml.edu%7C35ea5e2a7763468bdceb08daac84f785%7C4c25b8a617f746f983f054734ab81fb1%7C0%7C0%7C638011984335186283%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=jgKfndwNjtWPytb4psTSsGzSvuBzJyAlfQiutq4XrIo%3D&reserved=0> > ) > Alliance of Genome Resources Group Leader (http://alliancegenome.org/ > <https://nam10.safelinks.protection.outlook.com/?url=http%3A%2F%2Falliancegenome.org%2F&data=05%7C01%7COlivia_Rasmussen%40student.uml.edu%7C35ea5e2a7763468bdceb08daac84f785%7C4c25b8a617f746f983f054734ab81fb1%7C0%7C0%7C638011984335186283%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=gEE1xDPHnFX9AU3jAYMqQ1o07DdG9eqfGV%2BKGbToDYc%3D&reserved=0> > ) > VirusSeq Project Manager (https://virusseq-dataportal.ca/ > <https://nam10.safelinks.protection.outlook.com/?url=https%3A%2F%2Fvirusseq-dataportal.ca%2F&data=05%7C01%7COlivia_Rasmussen%40student.uml.edu%7C35ea5e2a7763468bdceb08daac84f785%7C4c25b8a617f746f983f054734ab81fb1%7C0%7C0%7C638011984335186283%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=NnJNItf5mJ0VzsmQIdSjH9dJO5YVmcK%2FvHF0uRr42g4%3D&reserved=0> > ) > Human Cancer Models Initiative Project Manager ( > https://hcmi-searchable-catalog.nci.nih.gov/ > <https://nam10.safelinks.protection.outlook.com/?url=https%3A%2F%2Fhcmi-searchable-catalog.nci.nih.gov%2F&data=05%7C01%7COlivia_Rasmussen%40student.uml.edu%7C35ea5e2a7763468bdceb08daac84f785%7C4c25b8a617f746f983f054734ab81fb1%7C0%7C0%7C638011984335186283%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=T0YcMeGE3ghiJt2xjIlgv5QI8FKtXzMGN7%2FVIA9zS6o%3D&reserved=0> > ) > -- ------------------------------------------------------------------------ Scott Cain, Ph. D. scott at scottcain dot net GMOD Project Manager (http://gmod.org/) 216-392-3087 WormBase Developer (http://wormbase.org/) Alliance of Genome Resources Group Leader (http://alliancegenome.org/) VirusSeq Project Manager (https://virusseq-dataportal.ca/) Human Cancer Models Initiative Project Manager ( https://hcmi-searchable-catalog.nci.nih.gov/) |
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From: Scott C. <sc...@sc...> - 2022-10-12 19:30:15
|
Hi Olivia, I'm wondering if you are the same person who asked a similar question on gitter. Either is fine with me; you're welcome to have the discussion anywhere you want :-) Scott On Wed, Oct 12, 2022 at 12:05 PM Rasmussen, Olivia < Oli...@st...> wrote: > Hello, > My name is Olivia and I am a student at Umass Lowell, currently working on > a research project which involves teaching high school students how to use > Jbrowse. > I am wondering gif there is a way to upload data directly from a URL? > Currently the data is on a one drive account and I have tried many times to > upload the links into the new track box but nothing ever works. We are > using BAM and BAI links. Wondering if you have any insight. > > Thanks, > Olivia > _______________________________________________ > Gmod-ajax mailing list > Gmo...@li... > https://lists.sourceforge.net/lists/listinfo/gmod-ajax > -- ------------------------------------------------------------------------ Scott Cain, Ph. D. scott at scottcain dot net GMOD Project Manager (http://gmod.org/) 216-392-3087 WormBase Developer (http://wormbase.org/) Alliance of Genome Resources Group Leader (http://alliancegenome.org/) VirusSeq Project Manager (https://virusseq-dataportal.ca/) Human Cancer Models Initiative Project Manager ( https://hcmi-searchable-catalog.nci.nih.gov/) |
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From: Rasmussen, O. <Oli...@st...> - 2022-10-12 18:58:28
|
Hello, My name is Olivia and I am a student at Umass Lowell, currently working on a research project which involves teaching high school students how to use Jbrowse. I am wondering gif there is a way to upload data directly from a URL? Currently the data is on a one drive account and I have tried many times to upload the links into the new track box but nothing ever works. We are using BAM and BAI links. Wondering if you have any insight. Thanks, Olivia |
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From: Scott C. <sc...@sc...> - 2022-09-01 16:52:02
|
Hi Priyanka, What version of JBrowse 2 are you using? That sort of error should have gone away as of about 1.6.0 (we are currently on 2.1.2). If you are at 1.6 or less, please try upgrading. Thanks, Scott On Thu, Sep 1, 2022 at 9:22 AM Priyanka Pandey <Pri...@bi...> wrote: > Dear JBrowse team, > > > > We have set-up JBrowse2 genome browser using Nginx server within a docker > container. In principle, things are working when we are zooming-in till > 736kbp. > > > > > > But when we zoom-out more than 750Kbp, we are getting errors (please see > below image as an example). > > > > > > Kindly suggest how to solve this issue. > > > > Thanks and regards, > > Priyanka Pandey > > > > > > *Dr. Priyanka Pandey* > Scientist Bioinformatics > Bioinformatics Research & Development > Tel.: +49 6131 9084-7035 > E-Mail: Pri...@bi... > > > > *Anschrift:* > BioNTech SE > An der Goldgrube 12 > 55131 Mainz > Germany > > <https://www.linkedin.com/company/biontech-se/mycompany/> > <https://twitter.com/BioNTech_Group> > > *Sitz der Gesellschaft: *BioNTech SE, An der Goldgrube 12, 55131 Mainz, > Germany > Amtsgericht Mainz HRB 48720 • USt.-IdNr. DE 263 382 495 • EoriNr: DE > 1070347 > *Vorstand: *Prof. Dr. Ugur Sahin • Sean Marett • Dr. Sierk Poetting • > Ryan Richardson • Prof. Dr. Özlem Türeci • Jens Holstein > > The information contained in this email is intended for the personal and > confidential use of the addressee only. It may also contain privileged > information. If you are not the intended recipient then you are hereby > notified that you have received this document in error and that any review, > distribution or copying of this document is strictly prohibited. If you > have received this communication in error, please notify the sender. > *Please protect our environment and consider whether you need to print > this e-mail.* > _______________________________________________ > Gmod-ajax mailing list > Gmo...@li... > https://lists.sourceforge.net/lists/listinfo/gmod-ajax > -- ------------------------------------------------------------------------ Scott Cain, Ph. D. scott at scottcain dot net GMOD Project Manager (http://gmod.org/) 216-392-3087 WormBase Developer (http://wormbase.org/) Alliance of Genome Resources Group Leader (http://alliancegenome.org/) VirusSeq Project Manager (https://virusseq-dataportal.ca/) Human Cancer Models Initiative Project Manager ( https://hcmi-searchable-catalog.nci.nih.gov/) |
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From: Priyanka P. <Pri...@bi...> - 2022-09-01 10:16:55
|
Dear JBrowse team, We have set-up JBrowse2 genome browser using Nginx server within a docker container. In principle, things are working when we are zooming-in till 736kbp. [cid:image001.png@01D8BDFA.21BABEF0] But when we zoom-out more than 750Kbp, we are getting errors (please see below image as an example). [cid:image002.png@01D8BDFA.21BABEF0] Kindly suggest how to solve this issue. Thanks and regards, Priyanka Pandey Dr. Priyanka Pandey Scientist Bioinformatics Bioinformatics Research & Development Tel.: +49 6131 9084-7035 E-Mail: Pri...@bi... [cid:bn_c069c2d9-7d5b-464f-942a-ded037136dc5.png] Anschrift: BioNTech SE An der Goldgrube 12 55131 Mainz Germany [cid:linkedin_32x32_1cb4dd84-bfb3-452e-a4e5-086b773a6426.png]<https://www.linkedin.com/company/biontech-se/mycompany/> [cid:twitter_32x32_f6ddd4b9-8a9d-4238-88e0-2820a87d34ee.png] <https://twitter.com/BioNTech_Group> Sitz der Gesellschaft: BioNTech SE, An der Goldgrube 12, 55131 Mainz, Germany Amtsgericht Mainz HRB 48720 * USt.-IdNr. DE 263 382 495 * EoriNr: DE 1070347 Vorstand: Prof. Dr. Ugur Sahin * Sean Marett * Dr. Sierk Poetting * Ryan Richardson * Prof. Dr. ?zlem T?reci * Jens Holstein The information contained in this email is intended for the personal and confidential use of the addressee only. It may also contain privileged information. If you are not the intended recipient then you are hereby notified that you have received this document in error and that any review, distribution or copying of this document is strictly prohibited. If you have received this communication in error, please notify the sender. Please protect our environment and consider whether you need to print this e-mail. |
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From: Scott C. <sc...@sc...> - 2022-08-19 18:10:09
|
Hi Flora, I haven't used maker2jbrowse, but my naive suggestion is to try executing maker2jbrowse from one directory up (so in the main jbrowse directory), like: bin/maker2jbrowse <gff path> The only reason I suggest this is that's how I execute every other script that I use in JBrowse. There might be a built in assumption about where it's getting executed from. Scott On Fri, Aug 19, 2022 at 9:58 AM Flora Uesseler < flo...@un...> wrote: > Dear GMOD Team, > > I am trying to parse my maker-derived GFF to jbrowse with maker2jbrowse, > but keep running into the below issue. > > ./maker2jbrowse ~/annotation-workdir/maker-rounds/rnd2_v2.summary.gff >> Can't exec "prepare-refseqs.pl": No such file or directory at >> ./maker2jbrowse line 280. >> prepare-refseqs.pl failed with exit status -1 at ./maker2jbrowse line >> 280. >> > > I managed to run prepare-refseqs.pl on its own succesfully. > Can you advise a way around this error? > > The version I am using is JBrowse-1.16.11, downloaded as a zipfile from > https://jbrowse.org/blog/ > I just unzipped and tried using the maker2jbrowse script in the /bin > directory. I tried both with the minified release and the dev version. > > My best, > Flora > > > _______________________________________________ > Gmod-ajax mailing list > Gmo...@li... > https://lists.sourceforge.net/lists/listinfo/gmod-ajax > -- ------------------------------------------------------------------------ Scott Cain, Ph. D. scott at scottcain dot net GMOD Project Manager (http://gmod.org/) 216-392-3087 WormBase Developer (http://wormbase.org/) Alliance of Genome Resources Group Leader (http://alliancegenome.org/) VirusSeq Project Manager (https://virusseq-dataportal.ca/) Human Cancer Models Initiative Project Manager ( https://hcmi-searchable-catalog.nci.nih.gov/) |
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From: Nathan D. <nd...@gm...> - 2022-08-19 16:52:27
|
Maybe set the type to Alignments2? (Canvas).
Nathan
> Begin forwarded message:
>
> From: Michał T. Lorenc <m.t...@gm... <mailto:m.t...@gm...>>
> Subject: [apollo] BAM file track
> Date: August 18, 2022 at 9:50:30 PM PDT
> To: apollo <ap...@lb... <mailto:ap...@lb...>>
>
> Hi all,
> The first BAM track comes from Star Aligner.
>
>
>
> {
> "storeClass": "JBrowse/Store/SeqFeature/BAM",
> "urlTemplate": "raw/Flower_BAM.bam",
> "style": {"className": "feature"},
> "label": "Flower_BAM",
> "apollo": {
> "source": "upload",
> "type": "BAM"
> },
> "type": "JBrowse/View/Track/Alignments",
> "category": "v. RNA-seq aligned reads",
> "key": "Flower_BAM"
> },
>
> This one comes from Hi-sat2 aligner.
>
>
>
>
> {
> "key" : "NbRNASeq_Meristem_Feb2019",
> "label" : "NbRNASeq_Meristem_Feb2019",
> "storeClass" : "JBrowse/Store/SeqFeature/BAM",
> "type" : "JBrowse/View/Track/Alignments",
> "urlTemplate" : "NbRNASeq_MstS.sorted.bam",
> "category" : "vi. Tracks Dev"
> },
>
> How do I get the Star Aligner to look like a Hi-sat2 track?
>
> Thank you in advance,
>
> Best wishes,
>
> Michal
>
> --
> To unsubscribe from this group and stop receiving emails from it, send an email to apo...@lb... <mailto:apo...@lb...>.
|
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From: Flora U. <flo...@un...> - 2022-08-19 10:55:03
|
Dear GMOD Team, I am trying to parse my maker-derived GFF to jbrowse with maker2jbrowse, but keep running into the below issue. ./maker2jbrowse ~/annotation-workdir/maker-rounds/rnd2_v2.summary.gff > Can't exec "prepare-refseqs.pl": No such file or directory at > ./maker2jbrowse line 280. > prepare-refseqs.pl failed with exit status -1 at ./maker2jbrowse line 280. > I managed to run prepare-refseqs.pl on its own succesfully. Can you advise a way around this error? The version I am using is JBrowse-1.16.11, downloaded as a zipfile from https://jbrowse.org/blog/ I just unzipped and tried using the maker2jbrowse script in the /bin directory. I tried both with the minified release and the dev version. My best, Flora |
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From: Garrett S. <ste...@gm...> - 2022-08-16 16:46:20
|
Hi Carlo, It's not possible to remove tracks with the CLI currently, but we do have an open issue you can follow here if you'd like: https://github.com/GMOD/jbrowse-components/issues/1253. You also can open your config.json file and remove the entry for that track if that works for you. Best, Garrett On Mon, Aug 15, 2022 at 9:14 PM Carlo Kroll <ckr...@gm...> wrote: > Dear Jbrowse Team, > > thank you for this great tool! I am just wondering whether there is the > possibility to delete assemblies or tracks with the command line interface? > I know it is possible with the Jbrowse Admin-server but is it also possible > without? > > Kind regards, > Carlo ( a very happy user :)) > _______________________________________________ > Gmod-ajax mailing list > Gmo...@li... > https://lists.sourceforge.net/lists/listinfo/gmod-ajax > |
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From: Carlo K. <ckr...@gm...> - 2022-08-15 07:38:30
|
Dear Jbrowse Team, thank you for this great tool! I am just wondering whether there is the possibility to delete assemblies or tracks with the command line interface? I know it is possible with the Jbrowse Admin-server but is it also possible without? Kind regards, Carlo ( a very happy user :)) |
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From: Ke J. <bio...@gm...> - 2022-08-05 13:21:29
|
It works! Thanks for the help! I think maybe we need to make the
documentation more detailed, about the attributes that could be used here.
For now it only mentions "group" and "color".
Ke
On Thu, Aug 4, 2022 at 4:59 PM Garrett Stevens <ste...@gm...>
wrote:
> Hmm, that might be a bug. Can you try using "source" instead of "name" and
> see if it works?
>
> Best,
> Garrett
>
> On Thu, Aug 4, 2022 at 8:39 AM Ke Jiang <bio...@gm...> wrote:
>
>> Hi,
>>
>> Thanks! I was trying to generate configurations on the backend to make
>> the tracks on the server side. I did more trying and here is what I found:
>>
>> The following configuration does not load local BigWig files (404 error
>> on JBrowse2 page):
>>
>> {
>> "type": "MultiQuantitativeTrack",
>> "trackId": "transcriptomes",
>> "name": "transcriptomes",
>> "category": ["mRNASeq", "MultiCoverage"],
>> "assemblyNames": ["Porcine S. scrofa v11.1"],
>> "adapter": {
>> "type": "MultiWiggleAdapter",
>> "bigWigs": [
>> "data/porcine/Sscrofa11/mRNASeq/transcritpome/SRR11185045.bw",
>> "data/porcine/Sscrofa11/mRNASeq/transcritpome/SRR11185045.bw"
>> ]
>> }
>> }
>>
>> But the following configuration works with "subadaptors", note the path
>> to the BigWig files did not change, still relative to the JBrowse2 home
>> directory:
>>
>> {
>> "type": "MultiQuantitativeTrack",
>> "trackId": "transcriptomes",
>> "name": "transcriptomes",
>> "category": ["mRNASeq", "MultiCoverage"],
>> "assemblyNames": ["Porcine S. scrofa v11.1"],
>> "adapter": {
>> "type": "MultiWiggleAdapter",
>> "subadapters": [
>> {
>> "type": "BigWigAdapter",
>> "bigWigLocation": {
>> "uri":
>> "data/porcine/Sscrofa11/mRNASeq/transcritpome/SRR11185045.bw"
>> },
>> "group": "infection",
>> "color": "#311b92"
>> },
>> {
>> "type": "BigWigAdapter",
>> "bigWigLocation": {
>> "uri":
>> "data/porcine/Sscrofa11/mRNASeq/transcritpome/SRR11185046.bw"
>> },
>> "group": "infection",
>> "color": "#311b92"
>> }
>> ]
>> }
>> }
>>
>> But I have an additional problem: now the subtracks have random names,
>> whenever I add the "name" attribute to the configuration, the coverage
>> plots disappear. For example, when I use the following:
>>
>> {
>> "type": "MultiQuantitativeTrack",
>> "trackId": "transcriptomes",
>> "name": "transcriptomes",
>> "category": ["mRNASeq", "MultiCoverage"],
>> "assemblyNames": ["Porcine S. scrofa v11.1"],
>> "adapter": {
>> "type": "MultiWiggleAdapter",
>> "subadapters": [
>> {
>> "type": "BigWigAdapter",
>> "bigWigLocation": {
>> "uri":
>> "data/porcine/Sscrofa11/mRNASeq/transcritpome/SRR11185045.bw"
>> },
>> "group": "infection",
>> "color": "#311b92",
>> "name": "SRR11185045"
>> },
>> {
>> "type": "BigWigAdapter",
>> "bigWigLocation": {
>> "uri":
>> "data/porcine/Sscrofa11/mRNASeq/transcritpome/SRR11185046.bw"
>> },
>> "group": "infection",
>> "color": "#311b92",
>> "name": "SRR11185046"
>> }
>> ]
>> }
>> }
>>
>> The names and tracks seem to be loading fine and there are no error
>> messages, but the coverage plots are gone, with only blank tracks.
>>
>> Any suggestions are welcome!
>>
>> Thanks!
>>
>> Ke
>>
>>
>>
>> On Wed, Aug 3, 2022 at 8:02 PM Garrett Stevens <
>> ste...@gm...> wrote:
>>
>>> Are you making a track config by hand or creating a multi-wiggle track
>>> in the UI? If you have the config, could you show us what it looks like?
>>>
>>> I think if you use the "subadapters" pattern described here
>>> <https://jbrowse.org/jb2/docs/config_guide/#general-multiquantitativetrack-options>,
>>> you should be able to get local files to load.
>>>
>>> Best,
>>> Garrett
>>>
>>> On Wed, Aug 3, 2022 at 4:58 PM Ke Jiang <bio...@gm...> wrote:
>>>
>>>> Hi,
>>>>
>>>> It was great to see the MultiBigWig feature get implemented. It was one
>>>> of few of the JBrowse1 features I missed most. Thanks for the hard work by
>>>> the developers! I do have a small problem when trying it out. Looks like
>>>> the adaptor could not deal with local BigWig files, even though the regular
>>>> single bigwig adaptor could. So when I use this path for my single BW track
>>>> it works:
>>>>
>>>> data/reference/mRNASeq/XXXX_transcritpome/XXXX.bw
>>>>
>>>> where the "data" directory is under the JBrowse home directory.
>>>>
>>>> But the same path does not work for the multibigwig configuration.
>>>>
>>>> For security reasons, we could not host the BW files via https, so it
>>>> would be best that local BW could be loaded, in the same way as the single
>>>> BW tracks. Any advice here?
>>>>
>>>> Thanks!
>>>>
>>>> Ke
>>>> _______________________________________________
>>>> Gmod-ajax mailing list
>>>> Gmo...@li...
>>>> https://lists.sourceforge.net/lists/listinfo/gmod-ajax
>>>>
>>>
|
|
From: Chen X. <xi...@ev...> - 2022-08-05 02:34:50
|
Hi Garrett,
Thanks for your explanation!
Best wishes,
Chen
----- 原始邮件 -----
发件人: "Garrett Stevens" <ste...@gm...>
收件人: "Chen Xie" <xi...@ev...>
抄送: "gmod-ajax" <gmo...@li...>
发送时间: 星期五, 2022年 8 月 05日 上午 5:50:51
主题: Re: [Gmod-ajax] About coloring tabix-indexed BED or bigBed tracks
Hi Chen,
I think it has to do with what you are coloring. In the ArcRenderer, the
arc is based on the top-level parent feature (e.g. a gene) where in the
SvgFeatureRenderer you are coloring a child feature (e.g. an mRNA), so you
have to retrieve the parent feature that has the itemRgb first.
Best,
Garrett
On Wed, Aug 3, 2022 at 8:54 PM Chen Xie <xi...@ev...> wrote:
> Hi Garrett,
>
> Thank you very much for your help! The problem is solved, but a bit
> different.
>
> For ArcRenderer, "color": "jexl:get(feature, 'itemRgb')" works, but
> "color": "jexl:get(parent(feature), 'itemRgb')" gives errors: "TypeError: e
> is undefined" for Firefox, and "TypeError: Cannot read properties of
> undefined (reading 'get')" for Chrome. However, for SvgFeatureRenderer (in
> the case of LinearBasicDisplay), "color1": "jexl:get(parent(feature),
> 'itemRgb')" works. Do you know the reason?
>
> Best wishes,
> Chen
>
>
>
>
> ----- 原始邮件 -----
> 发件人: "Garrett Stevens" <ste...@gm...>
> 收件人: "Chen Xie" <xi...@ev...>
> 抄送: "gmod-ajax" <gmo...@li...>
> 发送时间: 星期四, 2022年 8 月 04日 上午 8:33:36
> 主题: Re: [Gmod-ajax] About coloring tabix-indexed BED or bigBed tracks
>
> I might be able to help with this. The format of the arc renderer is
> different, so you'd have to have something like this for that display:
>
> {
> "type": "LinearArcDisplay",
> "displayId": "K562_bulk_co_sites_arc_color",
> "renderer": {
> "type": "ArcRenderer",
> "color": "jexl:get(parent(feature), 'itemRgb')"
> }
> }
>
> Note the different renderer type and "color" instead of "color1".
>
> Hope that helps,
> Garrett
>
> On Tue, Aug 2, 2022 at 11:01 PM Chen Xie <xi...@ev...> wrote:
>
> > Hi Colin,
> >
> > Thank you very much for your quick reply! Your suggestion works, but not
> > completely. If I do not add color configuration, such as:
> >
> > "displays": [
> > {
> > "type": "LinearArcDisplay",
> > "displayId": "K562_bulk_co_sites_arc_color"
> > },
> > {
> > "type": "LinearBasicDisplay",
> > "displayId": "K562_bulk_co_sites_basic_color",
> > "renderer": {
> > "type": "SvgFeatureRenderer",
> > "color1": "jexl:get(parent(feature), 'itemRgb')"
> > }
> > }
> > ],
> >
> > It works. But when I add color configuration, it does not work. For
> > example:
> >
> > "displays": [
> > {
> > "type": "LinearArcDisplay",
> > "displayId": "K562_bulk_co_sites_arc_color",
> > "renderer": {
> > "type": "SvgFeatureRenderer",
> > "color1": "jexl:get(parent(feature), 'itemRgb')"
> > }
> > },
> > {
> > "type": "LinearBasicDisplay",
> > "displayId": "K562_bulk_co_sites_basic_color",
> > "renderer": {
> > "type": "SvgFeatureRenderer",
> > "color1": "jexl:get(parent(feature), 'itemRgb')"
> > }
> > }
> > ],
> >
> > I tried with both v1.7.10 and v2.1.0. Could you please help me on this?
> > Thanks again!
> >
> > Best wishes,
> > Chen
> >
> >
> >
> >
> > ----- 原始邮件 -----
> > 发件人: "Colin" <col...@gm...>
> > 收件人: "Chen Xie" <xi...@ev...>
> > 抄送: "gmod-ajax" <gmo...@li...>
> > 发送时间: 星期二, 2022年 8 月 02日 下午 7:10:33
> > 主题: Re: [Gmod-ajax] About coloring tabix-indexed BED or bigBed tracks
> >
> > Hi there, there was a bug in the v2.0.0 release that caused this issue,
> we
> > will have it fixed in the next release
> > https://github.com/GMOD/jbrowse-components/pull/3120
> >
> > To hardcode a displaytype as the default, it can be listed as first in
> the
> > "displays" array in the config, example:
> >
> >
> > { "type": "FeatureTrack", "trackId": "gff3tabix_genes", "name":
> "GFF3Tabix
> > genes", "assemblyNames": [ "volvox" ], "adapter": { "type":
> > "Gff3TabixAdapter", "gffGzLocation": { "uri": "volvox.sort.gff3.gz" },
> > "index": { "location": { "uri": "volvox.sort.gff3.gz.tbi" } } },
> > "displays": [
> > { "type": "LinearArcDisplay", "displayId":
> > "gff3tabix_genes-LinearArcDisplay" }, { "type": "LinearBasicDisplay",
> > "displayId": "gff3tabix_genes-LinearBasicDisplay" } ] }
> >
> >
> > -Colin
> >
> > On Mon, Aug 1, 2022 at 9:05 PM Chen Xie <xi...@ev...> wrote:
> >
> > > Hi Colin,
> > >
> > > Thank you for helping us on coloring tabix-indexed BED tracks. Here is
> a
> > > related question. The JBrowse version we set up before was 1.7.10, and
> > now
> > > I notice that the lastest version is 2.1.0. However, when I upgraded
> our
> > > JBrowse to 2.1.0, LinearArcDisplay did not work anymore, i.e., nothing
> > > happened when I clicked "LinearArcDisplay". The reason that I would
> like
> > to
> > > upgrade and try LinearArcDisplay for tabix-indexed BED tracks is as you
> > > mentioned, coloring tracks in LinearArcDisplay might be possible in the
> > > newer versions. Thus, could you please also show me how to config this
> in
> > > the "config.json" file? Thanks again!
> > >
> > > Best wishes,
> > > Chen
> > >
> > >
> > >
> > >
> > > ----- 原始邮件 -----
> > > 发件人: "Chen Xie" <xi...@ev...>
> > > 收件人: "Colin" <col...@gm...>
> > > 抄送: "gmod-ajax" <gmo...@li...>
> > > 发送时间: 星期五, 2022年 6 月 24日 下午 4:02:57
> > > 主题: Re: [Gmod-ajax] About coloring tabix-indexed BED or bigBed tracks
> > >
> > > Hi Colin,
> > >
> > > It works! Thank you very much, and look forward to your updates on
> > > LinearArcDisplay and bigInteract in future.
> > >
> > > Best wishes,
> > > Chen
> > >
> > >
> > >
> > >
> > > ----- 原始邮件 -----
> > > 发件人: "Colin" <col...@gm...>
> > > 收件人: "Chen Xie" <xi...@ev...>
> > > 抄送: "gmod-ajax" <gmo...@li...>
> > > 发送时间: 星期五, 2022年 6 月 24日 下午 2:07:36
> > > 主题: Re: [Gmod-ajax] About coloring tabix-indexed BED or bigBed tracks
> > >
> > > If I am reading the screenshot correctly, this is helpful to see.
> > >
> > > The reason for the issue you are seeing is because jbrowse "synthesizes
> > > child features" from the bigBed feature, and so you would actually want
> > to
> > > access the parent feature's itemRgb field.
> > >
> > > Here is an example
> > >
> > > get(parent(feature),'itemRgb')
> > >
> > > This get's the parent feature's itemRgv field. Another helpful thing
> for
> > > debugging you can try is
> > >
> > > get(parent(log(feature)),'itemRgb')
> > >
> > > This is exactly the same as above, but it console.log's the feature so
> > you
> > > can inspect it in the chrome devtools :)
> > >
> > > Potentially we could transfer the parent feature data fields onto the
> > child
> > > feature to help with this case, or make a utility function that
> > > automatically looks at current and parent feature or something like
> that.
> > > Hope that helps though!
> > >
> > >
> > > -Colin
> > >
> > > On Thu, Jun 23, 2022 at 11:01 PM Chen Xie <xi...@ev...> wrote:
> > >
> > > > Hi Colin,
> > > >
> > > > Thank you very much for your nice reply! But after trying a lot in
> the
> > > > past days, I still have the same problem. As the example you can see
> in
> > > the
> > > > attached picture, everything is blue including the ones should be
> red.
> > > The
> > > > collumn name must be correct because I also tested with mouse over
> (see
> > > the
> > > > red rectangels). Could you please help me to figure out the reason?
> > > Thanks
> > > > again!
> > > >
> > > > Best wishes,
> > > > Chen
> > > >
> > > >
> > > >
> > > >
> > > > ----- 原始邮件 -----
> > > > 发件人: "Colin" <col...@gm...>
> > > > 收件人: "Chen Xie" <xi...@ev...>
> > > > 抄送: "gmod-ajax" <gmo...@li...>
> > > > 发送时间: 星期三, 2022年 6 月 22日 上午 2:02:04
> > > > 主题: Re: [Gmod-ajax] About coloring tabix-indexed BED or bigBed tracks
> > > >
> > > > Hi Chen
> > > > Great questions
> > > >
> > > > For the color callback, I think you have the right idea. The "field8"
> > > would
> > > > be an autoassigned name if the columns of your bed file do not have
> > > names.
> > > > If you have bigBed, you may have column names (they are often
> provided
> > by
> > > > an autoSql file). You can check the column names using bigBedInfo or
> > the
> > > > "About track" inside jbrowse 2. Then just swap out field8 for
> whatever
> > > the
> > > > column name is. Let me know if this still has issues
> > > >
> > > > For the other questions
> > > >
> > > > 1) Looks like currently LinearArcDisplay does not have a color
> > callback,
> > > we
> > > > will add this!
> > > > 2) I think bigInteract would be a great thing to try to make an
> example
> > > of
> > > > for our docs. I think if you wanted to, you could load a bigInteract
> > > bigBed
> > > > file, and use LinearArcDisplay, and it would generally work. The
> > features
> > > > of bigInteract that would be missing are the "feet" (e.g. the lines
> at
> > > > each end of arc here
> > > > https://genome.ucsc.edu/images/interactUnderstanding2.png) would be
> > > > missing, and the interchromosomal indicators would not display
> > > >
> > > > -Colin
> > > >
> > > >
> > > >
> > > >
> > > > On Tue, Jun 21, 2022 at 12:52 AM Chen Xie <xi...@ev...>
> wrote:
> > > >
> > > > > Dear Madam/Sir,
> > > > >
> > > > > We have installed your JBrowse 2 on our server to visualize our
> > > > sequencing
> > > > > data. Currently, we met a problem about coloring tabix-indexed BED
> or
> > > > > bigBed tracks. We put RGB values at the 9th column, and tried by
> > > > following "
> > > > > https://github.com/GMOD/jbrowse-components/discussions/2561" and "
> > > > > https://github.com/GMOD/jbrowse-components/discussions/2772", but
> it
> > > did
> > > > > not work. Our configuration in "config.json" is similar to (we
> tested
> > > > with
> > > > > many small changes):
> > > > >
> > > > > "displays": [
> > > > > {
> > > > > "type": "LinearBasicDisplay",
> > > > > "displayId": "color_test",
> > > > > "renderer": {
> > > > > "type": "SvgFeatureRenderer",
> > > > > "color1": "jexl:get(feature,
> > > > 'field8')=='255,0,0'?'red':'blue'"
> > > > > }
> > > > > }
> > > > > ],
> > > > >
> > > > > With the codes above, it always shows blue color, even when the
> > itemRgb
> > > > > column is '255,0,0', and we also tried with 'field9', but it did
> not
> > > work
> > > > > either. I guess that we did not put the correct name of the feature
> > > > there.
> > > > > Could you please help us on it?
> > > > >
> > > > > Here are two further quesions:
> > > > >
> > > > > 1. It is great to have this "LinearArcDisplay" in JBrowse 2, can we
> > > also
> > > > > color lines in this type of display?
> > > > >
> > > > > 2. We would like to visualize data in the format of UCSC interact
> ("
> > > > > https://genome.ucsc.edu/goldenPath/help/interact.html"), which is
> > > > > actually similar to your LinearArcDisplay. Do you plan to support
> it?
> > > > >
> > > > > Thank you very much and look forward to your reply!
> > > > >
> > > > > Best wishes,
> > > > > Chen Xie
> > > > >
> > > > >
> > > > >
> > > > >
> > > > >
> > > > > _______________________________________________
> > > > > Gmod-ajax mailing list
> > > > > Gmo...@li...
> > > > > https://lists.sourceforge.net/lists/listinfo/gmod-ajax
> > > > >
> > >
> >
> >
> > _______________________________________________
> > Gmod-ajax mailing list
> > Gmo...@li...
> > https://lists.sourceforge.net/lists/listinfo/gmod-ajax
> >
>
|
|
From: Garrett S. <ste...@gm...> - 2022-08-04 21:59:51
|
Hmm, that might be a bug. Can you try using "source" instead of "name" and
see if it works?
Best,
Garrett
On Thu, Aug 4, 2022 at 8:39 AM Ke Jiang <bio...@gm...> wrote:
> Hi,
>
> Thanks! I was trying to generate configurations on the backend to make the
> tracks on the server side. I did more trying and here is what I found:
>
> The following configuration does not load local BigWig files (404 error on
> JBrowse2 page):
>
> {
> "type": "MultiQuantitativeTrack",
> "trackId": "transcriptomes",
> "name": "transcriptomes",
> "category": ["mRNASeq", "MultiCoverage"],
> "assemblyNames": ["Porcine S. scrofa v11.1"],
> "adapter": {
> "type": "MultiWiggleAdapter",
> "bigWigs": [
> "data/porcine/Sscrofa11/mRNASeq/transcritpome/SRR11185045.bw",
> "data/porcine/Sscrofa11/mRNASeq/transcritpome/SRR11185045.bw"
> ]
> }
> }
>
> But the following configuration works with "subadaptors", note the path to
> the BigWig files did not change, still relative to the JBrowse2 home
> directory:
>
> {
> "type": "MultiQuantitativeTrack",
> "trackId": "transcriptomes",
> "name": "transcriptomes",
> "category": ["mRNASeq", "MultiCoverage"],
> "assemblyNames": ["Porcine S. scrofa v11.1"],
> "adapter": {
> "type": "MultiWiggleAdapter",
> "subadapters": [
> {
> "type": "BigWigAdapter",
> "bigWigLocation": {
> "uri":
> "data/porcine/Sscrofa11/mRNASeq/transcritpome/SRR11185045.bw"
> },
> "group": "infection",
> "color": "#311b92"
> },
> {
> "type": "BigWigAdapter",
> "bigWigLocation": {
> "uri":
> "data/porcine/Sscrofa11/mRNASeq/transcritpome/SRR11185046.bw"
> },
> "group": "infection",
> "color": "#311b92"
> }
> ]
> }
> }
>
> But I have an additional problem: now the subtracks have random names,
> whenever I add the "name" attribute to the configuration, the coverage
> plots disappear. For example, when I use the following:
>
> {
> "type": "MultiQuantitativeTrack",
> "trackId": "transcriptomes",
> "name": "transcriptomes",
> "category": ["mRNASeq", "MultiCoverage"],
> "assemblyNames": ["Porcine S. scrofa v11.1"],
> "adapter": {
> "type": "MultiWiggleAdapter",
> "subadapters": [
> {
> "type": "BigWigAdapter",
> "bigWigLocation": {
> "uri":
> "data/porcine/Sscrofa11/mRNASeq/transcritpome/SRR11185045.bw"
> },
> "group": "infection",
> "color": "#311b92",
> "name": "SRR11185045"
> },
> {
> "type": "BigWigAdapter",
> "bigWigLocation": {
> "uri":
> "data/porcine/Sscrofa11/mRNASeq/transcritpome/SRR11185046.bw"
> },
> "group": "infection",
> "color": "#311b92",
> "name": "SRR11185046"
> }
> ]
> }
> }
>
> The names and tracks seem to be loading fine and there are no error
> messages, but the coverage plots are gone, with only blank tracks.
>
> Any suggestions are welcome!
>
> Thanks!
>
> Ke
>
>
>
> On Wed, Aug 3, 2022 at 8:02 PM Garrett Stevens <
> ste...@gm...> wrote:
>
>> Are you making a track config by hand or creating a multi-wiggle track in
>> the UI? If you have the config, could you show us what it looks like?
>>
>> I think if you use the "subadapters" pattern described here
>> <https://jbrowse.org/jb2/docs/config_guide/#general-multiquantitativetrack-options>,
>> you should be able to get local files to load.
>>
>> Best,
>> Garrett
>>
>> On Wed, Aug 3, 2022 at 4:58 PM Ke Jiang <bio...@gm...> wrote:
>>
>>> Hi,
>>>
>>> It was great to see the MultiBigWig feature get implemented. It was one
>>> of few of the JBrowse1 features I missed most. Thanks for the hard work by
>>> the developers! I do have a small problem when trying it out. Looks like
>>> the adaptor could not deal with local BigWig files, even though the regular
>>> single bigwig adaptor could. So when I use this path for my single BW track
>>> it works:
>>>
>>> data/reference/mRNASeq/XXXX_transcritpome/XXXX.bw
>>>
>>> where the "data" directory is under the JBrowse home directory.
>>>
>>> But the same path does not work for the multibigwig configuration.
>>>
>>> For security reasons, we could not host the BW files via https, so it
>>> would be best that local BW could be loaded, in the same way as the single
>>> BW tracks. Any advice here?
>>>
>>> Thanks!
>>>
>>> Ke
>>> _______________________________________________
>>> Gmod-ajax mailing list
>>> Gmo...@li...
>>> https://lists.sourceforge.net/lists/listinfo/gmod-ajax
>>>
>>
|
|
From: Garrett S. <ste...@gm...> - 2022-08-04 21:51:14
|
Hi Chen,
I think it has to do with what you are coloring. In the ArcRenderer, the
arc is based on the top-level parent feature (e.g. a gene) where in the
SvgFeatureRenderer you are coloring a child feature (e.g. an mRNA), so you
have to retrieve the parent feature that has the itemRgb first.
Best,
Garrett
On Wed, Aug 3, 2022 at 8:54 PM Chen Xie <xi...@ev...> wrote:
> Hi Garrett,
>
> Thank you very much for your help! The problem is solved, but a bit
> different.
>
> For ArcRenderer, "color": "jexl:get(feature, 'itemRgb')" works, but
> "color": "jexl:get(parent(feature), 'itemRgb')" gives errors: "TypeError: e
> is undefined" for Firefox, and "TypeError: Cannot read properties of
> undefined (reading 'get')" for Chrome. However, for SvgFeatureRenderer (in
> the case of LinearBasicDisplay), "color1": "jexl:get(parent(feature),
> 'itemRgb')" works. Do you know the reason?
>
> Best wishes,
> Chen
>
>
>
>
> ----- 原始邮件 -----
> 发件人: "Garrett Stevens" <ste...@gm...>
> 收件人: "Chen Xie" <xi...@ev...>
> 抄送: "gmod-ajax" <gmo...@li...>
> 发送时间: 星期四, 2022年 8 月 04日 上午 8:33:36
> 主题: Re: [Gmod-ajax] About coloring tabix-indexed BED or bigBed tracks
>
> I might be able to help with this. The format of the arc renderer is
> different, so you'd have to have something like this for that display:
>
> {
> "type": "LinearArcDisplay",
> "displayId": "K562_bulk_co_sites_arc_color",
> "renderer": {
> "type": "ArcRenderer",
> "color": "jexl:get(parent(feature), 'itemRgb')"
> }
> }
>
> Note the different renderer type and "color" instead of "color1".
>
> Hope that helps,
> Garrett
>
> On Tue, Aug 2, 2022 at 11:01 PM Chen Xie <xi...@ev...> wrote:
>
> > Hi Colin,
> >
> > Thank you very much for your quick reply! Your suggestion works, but not
> > completely. If I do not add color configuration, such as:
> >
> > "displays": [
> > {
> > "type": "LinearArcDisplay",
> > "displayId": "K562_bulk_co_sites_arc_color"
> > },
> > {
> > "type": "LinearBasicDisplay",
> > "displayId": "K562_bulk_co_sites_basic_color",
> > "renderer": {
> > "type": "SvgFeatureRenderer",
> > "color1": "jexl:get(parent(feature), 'itemRgb')"
> > }
> > }
> > ],
> >
> > It works. But when I add color configuration, it does not work. For
> > example:
> >
> > "displays": [
> > {
> > "type": "LinearArcDisplay",
> > "displayId": "K562_bulk_co_sites_arc_color",
> > "renderer": {
> > "type": "SvgFeatureRenderer",
> > "color1": "jexl:get(parent(feature), 'itemRgb')"
> > }
> > },
> > {
> > "type": "LinearBasicDisplay",
> > "displayId": "K562_bulk_co_sites_basic_color",
> > "renderer": {
> > "type": "SvgFeatureRenderer",
> > "color1": "jexl:get(parent(feature), 'itemRgb')"
> > }
> > }
> > ],
> >
> > I tried with both v1.7.10 and v2.1.0. Could you please help me on this?
> > Thanks again!
> >
> > Best wishes,
> > Chen
> >
> >
> >
> >
> > ----- 原始邮件 -----
> > 发件人: "Colin" <col...@gm...>
> > 收件人: "Chen Xie" <xi...@ev...>
> > 抄送: "gmod-ajax" <gmo...@li...>
> > 发送时间: 星期二, 2022年 8 月 02日 下午 7:10:33
> > 主题: Re: [Gmod-ajax] About coloring tabix-indexed BED or bigBed tracks
> >
> > Hi there, there was a bug in the v2.0.0 release that caused this issue,
> we
> > will have it fixed in the next release
> > https://github.com/GMOD/jbrowse-components/pull/3120
> >
> > To hardcode a displaytype as the default, it can be listed as first in
> the
> > "displays" array in the config, example:
> >
> >
> > { "type": "FeatureTrack", "trackId": "gff3tabix_genes", "name":
> "GFF3Tabix
> > genes", "assemblyNames": [ "volvox" ], "adapter": { "type":
> > "Gff3TabixAdapter", "gffGzLocation": { "uri": "volvox.sort.gff3.gz" },
> > "index": { "location": { "uri": "volvox.sort.gff3.gz.tbi" } } },
> > "displays": [
> > { "type": "LinearArcDisplay", "displayId":
> > "gff3tabix_genes-LinearArcDisplay" }, { "type": "LinearBasicDisplay",
> > "displayId": "gff3tabix_genes-LinearBasicDisplay" } ] }
> >
> >
> > -Colin
> >
> > On Mon, Aug 1, 2022 at 9:05 PM Chen Xie <xi...@ev...> wrote:
> >
> > > Hi Colin,
> > >
> > > Thank you for helping us on coloring tabix-indexed BED tracks. Here is
> a
> > > related question. The JBrowse version we set up before was 1.7.10, and
> > now
> > > I notice that the lastest version is 2.1.0. However, when I upgraded
> our
> > > JBrowse to 2.1.0, LinearArcDisplay did not work anymore, i.e., nothing
> > > happened when I clicked "LinearArcDisplay". The reason that I would
> like
> > to
> > > upgrade and try LinearArcDisplay for tabix-indexed BED tracks is as you
> > > mentioned, coloring tracks in LinearArcDisplay might be possible in the
> > > newer versions. Thus, could you please also show me how to config this
> in
> > > the "config.json" file? Thanks again!
> > >
> > > Best wishes,
> > > Chen
> > >
> > >
> > >
> > >
> > > ----- 原始邮件 -----
> > > 发件人: "Chen Xie" <xi...@ev...>
> > > 收件人: "Colin" <col...@gm...>
> > > 抄送: "gmod-ajax" <gmo...@li...>
> > > 发送时间: 星期五, 2022年 6 月 24日 下午 4:02:57
> > > 主题: Re: [Gmod-ajax] About coloring tabix-indexed BED or bigBed tracks
> > >
> > > Hi Colin,
> > >
> > > It works! Thank you very much, and look forward to your updates on
> > > LinearArcDisplay and bigInteract in future.
> > >
> > > Best wishes,
> > > Chen
> > >
> > >
> > >
> > >
> > > ----- 原始邮件 -----
> > > 发件人: "Colin" <col...@gm...>
> > > 收件人: "Chen Xie" <xi...@ev...>
> > > 抄送: "gmod-ajax" <gmo...@li...>
> > > 发送时间: 星期五, 2022年 6 月 24日 下午 2:07:36
> > > 主题: Re: [Gmod-ajax] About coloring tabix-indexed BED or bigBed tracks
> > >
> > > If I am reading the screenshot correctly, this is helpful to see.
> > >
> > > The reason for the issue you are seeing is because jbrowse "synthesizes
> > > child features" from the bigBed feature, and so you would actually want
> > to
> > > access the parent feature's itemRgb field.
> > >
> > > Here is an example
> > >
> > > get(parent(feature),'itemRgb')
> > >
> > > This get's the parent feature's itemRgv field. Another helpful thing
> for
> > > debugging you can try is
> > >
> > > get(parent(log(feature)),'itemRgb')
> > >
> > > This is exactly the same as above, but it console.log's the feature so
> > you
> > > can inspect it in the chrome devtools :)
> > >
> > > Potentially we could transfer the parent feature data fields onto the
> > child
> > > feature to help with this case, or make a utility function that
> > > automatically looks at current and parent feature or something like
> that.
> > > Hope that helps though!
> > >
> > >
> > > -Colin
> > >
> > > On Thu, Jun 23, 2022 at 11:01 PM Chen Xie <xi...@ev...> wrote:
> > >
> > > > Hi Colin,
> > > >
> > > > Thank you very much for your nice reply! But after trying a lot in
> the
> > > > past days, I still have the same problem. As the example you can see
> in
> > > the
> > > > attached picture, everything is blue including the ones should be
> red.
> > > The
> > > > collumn name must be correct because I also tested with mouse over
> (see
> > > the
> > > > red rectangels). Could you please help me to figure out the reason?
> > > Thanks
> > > > again!
> > > >
> > > > Best wishes,
> > > > Chen
> > > >
> > > >
> > > >
> > > >
> > > > ----- 原始邮件 -----
> > > > 发件人: "Colin" <col...@gm...>
> > > > 收件人: "Chen Xie" <xi...@ev...>
> > > > 抄送: "gmod-ajax" <gmo...@li...>
> > > > 发送时间: 星期三, 2022年 6 月 22日 上午 2:02:04
> > > > 主题: Re: [Gmod-ajax] About coloring tabix-indexed BED or bigBed tracks
> > > >
> > > > Hi Chen
> > > > Great questions
> > > >
> > > > For the color callback, I think you have the right idea. The "field8"
> > > would
> > > > be an autoassigned name if the columns of your bed file do not have
> > > names.
> > > > If you have bigBed, you may have column names (they are often
> provided
> > by
> > > > an autoSql file). You can check the column names using bigBedInfo or
> > the
> > > > "About track" inside jbrowse 2. Then just swap out field8 for
> whatever
> > > the
> > > > column name is. Let me know if this still has issues
> > > >
> > > > For the other questions
> > > >
> > > > 1) Looks like currently LinearArcDisplay does not have a color
> > callback,
> > > we
> > > > will add this!
> > > > 2) I think bigInteract would be a great thing to try to make an
> example
> > > of
> > > > for our docs. I think if you wanted to, you could load a bigInteract
> > > bigBed
> > > > file, and use LinearArcDisplay, and it would generally work. The
> > features
> > > > of bigInteract that would be missing are the "feet" (e.g. the lines
> at
> > > > each end of arc here
> > > > https://genome.ucsc.edu/images/interactUnderstanding2.png) would be
> > > > missing, and the interchromosomal indicators would not display
> > > >
> > > > -Colin
> > > >
> > > >
> > > >
> > > >
> > > > On Tue, Jun 21, 2022 at 12:52 AM Chen Xie <xi...@ev...>
> wrote:
> > > >
> > > > > Dear Madam/Sir,
> > > > >
> > > > > We have installed your JBrowse 2 on our server to visualize our
> > > > sequencing
> > > > > data. Currently, we met a problem about coloring tabix-indexed BED
> or
> > > > > bigBed tracks. We put RGB values at the 9th column, and tried by
> > > > following "
> > > > > https://github.com/GMOD/jbrowse-components/discussions/2561" and "
> > > > > https://github.com/GMOD/jbrowse-components/discussions/2772", but
> it
> > > did
> > > > > not work. Our configuration in "config.json" is similar to (we
> tested
> > > > with
> > > > > many small changes):
> > > > >
> > > > > "displays": [
> > > > > {
> > > > > "type": "LinearBasicDisplay",
> > > > > "displayId": "color_test",
> > > > > "renderer": {
> > > > > "type": "SvgFeatureRenderer",
> > > > > "color1": "jexl:get(feature,
> > > > 'field8')=='255,0,0'?'red':'blue'"
> > > > > }
> > > > > }
> > > > > ],
> > > > >
> > > > > With the codes above, it always shows blue color, even when the
> > itemRgb
> > > > > column is '255,0,0', and we also tried with 'field9', but it did
> not
> > > work
> > > > > either. I guess that we did not put the correct name of the feature
> > > > there.
> > > > > Could you please help us on it?
> > > > >
> > > > > Here are two further quesions:
> > > > >
> > > > > 1. It is great to have this "LinearArcDisplay" in JBrowse 2, can we
> > > also
> > > > > color lines in this type of display?
> > > > >
> > > > > 2. We would like to visualize data in the format of UCSC interact
> ("
> > > > > https://genome.ucsc.edu/goldenPath/help/interact.html"), which is
> > > > > actually similar to your LinearArcDisplay. Do you plan to support
> it?
> > > > >
> > > > > Thank you very much and look forward to your reply!
> > > > >
> > > > > Best wishes,
> > > > > Chen Xie
> > > > >
> > > > >
> > > > >
> > > > >
> > > > >
> > > > > _______________________________________________
> > > > > Gmod-ajax mailing list
> > > > > Gmo...@li...
> > > > > https://lists.sourceforge.net/lists/listinfo/gmod-ajax
> > > > >
> > >
> >
> >
> > _______________________________________________
> > Gmod-ajax mailing list
> > Gmo...@li...
> > https://lists.sourceforge.net/lists/listinfo/gmod-ajax
> >
>
|
|
From: Ke J. <bio...@gm...> - 2022-08-04 14:39:58
|
Hi,
Thanks! I was trying to generate configurations on the backend to make the
tracks on the server side. I did more trying and here is what I found:
The following configuration does not load local BigWig files (404 error on
JBrowse2 page):
{
"type": "MultiQuantitativeTrack",
"trackId": "transcriptomes",
"name": "transcriptomes",
"category": ["mRNASeq", "MultiCoverage"],
"assemblyNames": ["Porcine S. scrofa v11.1"],
"adapter": {
"type": "MultiWiggleAdapter",
"bigWigs": [
"data/porcine/Sscrofa11/mRNASeq/transcritpome/SRR11185045.bw",
"data/porcine/Sscrofa11/mRNASeq/transcritpome/SRR11185045.bw"
]
}
}
But the following configuration works with "subadaptors", note the path to
the BigWig files did not change, still relative to the JBrowse2 home
directory:
{
"type": "MultiQuantitativeTrack",
"trackId": "transcriptomes",
"name": "transcriptomes",
"category": ["mRNASeq", "MultiCoverage"],
"assemblyNames": ["Porcine S. scrofa v11.1"],
"adapter": {
"type": "MultiWiggleAdapter",
"subadapters": [
{
"type": "BigWigAdapter",
"bigWigLocation": {
"uri":
"data/porcine/Sscrofa11/mRNASeq/transcritpome/SRR11185045.bw"
},
"group": "infection",
"color": "#311b92"
},
{
"type": "BigWigAdapter",
"bigWigLocation": {
"uri":
"data/porcine/Sscrofa11/mRNASeq/transcritpome/SRR11185046.bw"
},
"group": "infection",
"color": "#311b92"
}
]
}
}
But I have an additional problem: now the subtracks have random names,
whenever I add the "name" attribute to the configuration, the coverage
plots disappear. For example, when I use the following:
{
"type": "MultiQuantitativeTrack",
"trackId": "transcriptomes",
"name": "transcriptomes",
"category": ["mRNASeq", "MultiCoverage"],
"assemblyNames": ["Porcine S. scrofa v11.1"],
"adapter": {
"type": "MultiWiggleAdapter",
"subadapters": [
{
"type": "BigWigAdapter",
"bigWigLocation": {
"uri":
"data/porcine/Sscrofa11/mRNASeq/transcritpome/SRR11185045.bw"
},
"group": "infection",
"color": "#311b92",
"name": "SRR11185045"
},
{
"type": "BigWigAdapter",
"bigWigLocation": {
"uri":
"data/porcine/Sscrofa11/mRNASeq/transcritpome/SRR11185046.bw"
},
"group": "infection",
"color": "#311b92",
"name": "SRR11185046"
}
]
}
}
The names and tracks seem to be loading fine and there are no error
messages, but the coverage plots are gone, with only blank tracks.
Any suggestions are welcome!
Thanks!
Ke
On Wed, Aug 3, 2022 at 8:02 PM Garrett Stevens <ste...@gm...>
wrote:
> Are you making a track config by hand or creating a multi-wiggle track in
> the UI? If you have the config, could you show us what it looks like?
>
> I think if you use the "subadapters" pattern described here
> <https://jbrowse.org/jb2/docs/config_guide/#general-multiquantitativetrack-options>,
> you should be able to get local files to load.
>
> Best,
> Garrett
>
> On Wed, Aug 3, 2022 at 4:58 PM Ke Jiang <bio...@gm...> wrote:
>
>> Hi,
>>
>> It was great to see the MultiBigWig feature get implemented. It was one
>> of few of the JBrowse1 features I missed most. Thanks for the hard work by
>> the developers! I do have a small problem when trying it out. Looks like
>> the adaptor could not deal with local BigWig files, even though the regular
>> single bigwig adaptor could. So when I use this path for my single BW track
>> it works:
>>
>> data/reference/mRNASeq/XXXX_transcritpome/XXXX.bw
>>
>> where the "data" directory is under the JBrowse home directory.
>>
>> But the same path does not work for the multibigwig configuration.
>>
>> For security reasons, we could not host the BW files via https, so it
>> would be best that local BW could be loaded, in the same way as the single
>> BW tracks. Any advice here?
>>
>> Thanks!
>>
>> Ke
>> _______________________________________________
>> Gmod-ajax mailing list
>> Gmo...@li...
>> https://lists.sourceforge.net/lists/listinfo/gmod-ajax
>>
>
|
|
From: Chen X. <xi...@ev...> - 2022-08-04 02:54:57
|
Hi Garrett,
Thank you very much for your help! The problem is solved, but a bit different.
For ArcRenderer, "color": "jexl:get(feature, 'itemRgb')" works, but "color": "jexl:get(parent(feature), 'itemRgb')" gives errors: "TypeError: e is undefined" for Firefox, and "TypeError: Cannot read properties of undefined (reading 'get')" for Chrome. However, for SvgFeatureRenderer (in the case of LinearBasicDisplay), "color1": "jexl:get(parent(feature), 'itemRgb')" works. Do you know the reason?
Best wishes,
Chen
----- 原始邮件 -----
发件人: "Garrett Stevens" <ste...@gm...>
收件人: "Chen Xie" <xi...@ev...>
抄送: "gmod-ajax" <gmo...@li...>
发送时间: 星期四, 2022年 8 月 04日 上午 8:33:36
主题: Re: [Gmod-ajax] About coloring tabix-indexed BED or bigBed tracks
I might be able to help with this. The format of the arc renderer is
different, so you'd have to have something like this for that display:
{
"type": "LinearArcDisplay",
"displayId": "K562_bulk_co_sites_arc_color",
"renderer": {
"type": "ArcRenderer",
"color": "jexl:get(parent(feature), 'itemRgb')"
}
}
Note the different renderer type and "color" instead of "color1".
Hope that helps,
Garrett
On Tue, Aug 2, 2022 at 11:01 PM Chen Xie <xi...@ev...> wrote:
> Hi Colin,
>
> Thank you very much for your quick reply! Your suggestion works, but not
> completely. If I do not add color configuration, such as:
>
> "displays": [
> {
> "type": "LinearArcDisplay",
> "displayId": "K562_bulk_co_sites_arc_color"
> },
> {
> "type": "LinearBasicDisplay",
> "displayId": "K562_bulk_co_sites_basic_color",
> "renderer": {
> "type": "SvgFeatureRenderer",
> "color1": "jexl:get(parent(feature), 'itemRgb')"
> }
> }
> ],
>
> It works. But when I add color configuration, it does not work. For
> example:
>
> "displays": [
> {
> "type": "LinearArcDisplay",
> "displayId": "K562_bulk_co_sites_arc_color",
> "renderer": {
> "type": "SvgFeatureRenderer",
> "color1": "jexl:get(parent(feature), 'itemRgb')"
> }
> },
> {
> "type": "LinearBasicDisplay",
> "displayId": "K562_bulk_co_sites_basic_color",
> "renderer": {
> "type": "SvgFeatureRenderer",
> "color1": "jexl:get(parent(feature), 'itemRgb')"
> }
> }
> ],
>
> I tried with both v1.7.10 and v2.1.0. Could you please help me on this?
> Thanks again!
>
> Best wishes,
> Chen
>
>
>
>
> ----- 原始邮件 -----
> 发件人: "Colin" <col...@gm...>
> 收件人: "Chen Xie" <xi...@ev...>
> 抄送: "gmod-ajax" <gmo...@li...>
> 发送时间: 星期二, 2022年 8 月 02日 下午 7:10:33
> 主题: Re: [Gmod-ajax] About coloring tabix-indexed BED or bigBed tracks
>
> Hi there, there was a bug in the v2.0.0 release that caused this issue, we
> will have it fixed in the next release
> https://github.com/GMOD/jbrowse-components/pull/3120
>
> To hardcode a displaytype as the default, it can be listed as first in the
> "displays" array in the config, example:
>
>
> { "type": "FeatureTrack", "trackId": "gff3tabix_genes", "name": "GFF3Tabix
> genes", "assemblyNames": [ "volvox" ], "adapter": { "type":
> "Gff3TabixAdapter", "gffGzLocation": { "uri": "volvox.sort.gff3.gz" },
> "index": { "location": { "uri": "volvox.sort.gff3.gz.tbi" } } },
> "displays": [
> { "type": "LinearArcDisplay", "displayId":
> "gff3tabix_genes-LinearArcDisplay" }, { "type": "LinearBasicDisplay",
> "displayId": "gff3tabix_genes-LinearBasicDisplay" } ] }
>
>
> -Colin
>
> On Mon, Aug 1, 2022 at 9:05 PM Chen Xie <xi...@ev...> wrote:
>
> > Hi Colin,
> >
> > Thank you for helping us on coloring tabix-indexed BED tracks. Here is a
> > related question. The JBrowse version we set up before was 1.7.10, and
> now
> > I notice that the lastest version is 2.1.0. However, when I upgraded our
> > JBrowse to 2.1.0, LinearArcDisplay did not work anymore, i.e., nothing
> > happened when I clicked "LinearArcDisplay". The reason that I would like
> to
> > upgrade and try LinearArcDisplay for tabix-indexed BED tracks is as you
> > mentioned, coloring tracks in LinearArcDisplay might be possible in the
> > newer versions. Thus, could you please also show me how to config this in
> > the "config.json" file? Thanks again!
> >
> > Best wishes,
> > Chen
> >
> >
> >
> >
> > ----- 原始邮件 -----
> > 发件人: "Chen Xie" <xi...@ev...>
> > 收件人: "Colin" <col...@gm...>
> > 抄送: "gmod-ajax" <gmo...@li...>
> > 发送时间: 星期五, 2022年 6 月 24日 下午 4:02:57
> > 主题: Re: [Gmod-ajax] About coloring tabix-indexed BED or bigBed tracks
> >
> > Hi Colin,
> >
> > It works! Thank you very much, and look forward to your updates on
> > LinearArcDisplay and bigInteract in future.
> >
> > Best wishes,
> > Chen
> >
> >
> >
> >
> > ----- 原始邮件 -----
> > 发件人: "Colin" <col...@gm...>
> > 收件人: "Chen Xie" <xi...@ev...>
> > 抄送: "gmod-ajax" <gmo...@li...>
> > 发送时间: 星期五, 2022年 6 月 24日 下午 2:07:36
> > 主题: Re: [Gmod-ajax] About coloring tabix-indexed BED or bigBed tracks
> >
> > If I am reading the screenshot correctly, this is helpful to see.
> >
> > The reason for the issue you are seeing is because jbrowse "synthesizes
> > child features" from the bigBed feature, and so you would actually want
> to
> > access the parent feature's itemRgb field.
> >
> > Here is an example
> >
> > get(parent(feature),'itemRgb')
> >
> > This get's the parent feature's itemRgv field. Another helpful thing for
> > debugging you can try is
> >
> > get(parent(log(feature)),'itemRgb')
> >
> > This is exactly the same as above, but it console.log's the feature so
> you
> > can inspect it in the chrome devtools :)
> >
> > Potentially we could transfer the parent feature data fields onto the
> child
> > feature to help with this case, or make a utility function that
> > automatically looks at current and parent feature or something like that.
> > Hope that helps though!
> >
> >
> > -Colin
> >
> > On Thu, Jun 23, 2022 at 11:01 PM Chen Xie <xi...@ev...> wrote:
> >
> > > Hi Colin,
> > >
> > > Thank you very much for your nice reply! But after trying a lot in the
> > > past days, I still have the same problem. As the example you can see in
> > the
> > > attached picture, everything is blue including the ones should be red.
> > The
> > > collumn name must be correct because I also tested with mouse over (see
> > the
> > > red rectangels). Could you please help me to figure out the reason?
> > Thanks
> > > again!
> > >
> > > Best wishes,
> > > Chen
> > >
> > >
> > >
> > >
> > > ----- 原始邮件 -----
> > > 发件人: "Colin" <col...@gm...>
> > > 收件人: "Chen Xie" <xi...@ev...>
> > > 抄送: "gmod-ajax" <gmo...@li...>
> > > 发送时间: 星期三, 2022年 6 月 22日 上午 2:02:04
> > > 主题: Re: [Gmod-ajax] About coloring tabix-indexed BED or bigBed tracks
> > >
> > > Hi Chen
> > > Great questions
> > >
> > > For the color callback, I think you have the right idea. The "field8"
> > would
> > > be an autoassigned name if the columns of your bed file do not have
> > names.
> > > If you have bigBed, you may have column names (they are often provided
> by
> > > an autoSql file). You can check the column names using bigBedInfo or
> the
> > > "About track" inside jbrowse 2. Then just swap out field8 for whatever
> > the
> > > column name is. Let me know if this still has issues
> > >
> > > For the other questions
> > >
> > > 1) Looks like currently LinearArcDisplay does not have a color
> callback,
> > we
> > > will add this!
> > > 2) I think bigInteract would be a great thing to try to make an example
> > of
> > > for our docs. I think if you wanted to, you could load a bigInteract
> > bigBed
> > > file, and use LinearArcDisplay, and it would generally work. The
> features
> > > of bigInteract that would be missing are the "feet" (e.g. the lines at
> > > each end of arc here
> > > https://genome.ucsc.edu/images/interactUnderstanding2.png) would be
> > > missing, and the interchromosomal indicators would not display
> > >
> > > -Colin
> > >
> > >
> > >
> > >
> > > On Tue, Jun 21, 2022 at 12:52 AM Chen Xie <xi...@ev...> wrote:
> > >
> > > > Dear Madam/Sir,
> > > >
> > > > We have installed your JBrowse 2 on our server to visualize our
> > > sequencing
> > > > data. Currently, we met a problem about coloring tabix-indexed BED or
> > > > bigBed tracks. We put RGB values at the 9th column, and tried by
> > > following "
> > > > https://github.com/GMOD/jbrowse-components/discussions/2561" and "
> > > > https://github.com/GMOD/jbrowse-components/discussions/2772", but it
> > did
> > > > not work. Our configuration in "config.json" is similar to (we tested
> > > with
> > > > many small changes):
> > > >
> > > > "displays": [
> > > > {
> > > > "type": "LinearBasicDisplay",
> > > > "displayId": "color_test",
> > > > "renderer": {
> > > > "type": "SvgFeatureRenderer",
> > > > "color1": "jexl:get(feature,
> > > 'field8')=='255,0,0'?'red':'blue'"
> > > > }
> > > > }
> > > > ],
> > > >
> > > > With the codes above, it always shows blue color, even when the
> itemRgb
> > > > column is '255,0,0', and we also tried with 'field9', but it did not
> > work
> > > > either. I guess that we did not put the correct name of the feature
> > > there.
> > > > Could you please help us on it?
> > > >
> > > > Here are two further quesions:
> > > >
> > > > 1. It is great to have this "LinearArcDisplay" in JBrowse 2, can we
> > also
> > > > color lines in this type of display?
> > > >
> > > > 2. We would like to visualize data in the format of UCSC interact ("
> > > > https://genome.ucsc.edu/goldenPath/help/interact.html"), which is
> > > > actually similar to your LinearArcDisplay. Do you plan to support it?
> > > >
> > > > Thank you very much and look forward to your reply!
> > > >
> > > > Best wishes,
> > > > Chen Xie
> > > >
> > > >
> > > >
> > > >
> > > >
> > > > _______________________________________________
> > > > Gmod-ajax mailing list
> > > > Gmo...@li...
> > > > https://lists.sourceforge.net/lists/listinfo/gmod-ajax
> > > >
> >
>
>
> _______________________________________________
> Gmod-ajax mailing list
> Gmo...@li...
> https://lists.sourceforge.net/lists/listinfo/gmod-ajax
>
|
|
From: Garrett S. <ste...@gm...> - 2022-08-04 01:02:40
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Are you making a track config by hand or creating a multi-wiggle track in the UI? If you have the config, could you show us what it looks like? I think if you use the "subadapters" pattern described here <https://jbrowse.org/jb2/docs/config_guide/#general-multiquantitativetrack-options>, you should be able to get local files to load. Best, Garrett On Wed, Aug 3, 2022 at 4:58 PM Ke Jiang <bio...@gm...> wrote: > Hi, > > It was great to see the MultiBigWig feature get implemented. It was one of > few of the JBrowse1 features I missed most. Thanks for the hard work by the > developers! I do have a small problem when trying it out. Looks like the > adaptor could not deal with local BigWig files, even though the regular > single bigwig adaptor could. So when I use this path for my single BW track > it works: > > data/reference/mRNASeq/XXXX_transcritpome/XXXX.bw > > where the "data" directory is under the JBrowse home directory. > > But the same path does not work for the multibigwig configuration. > > For security reasons, we could not host the BW files via https, so it > would be best that local BW could be loaded, in the same way as the single > BW tracks. Any advice here? > > Thanks! > > Ke > _______________________________________________ > Gmod-ajax mailing list > Gmo...@li... > https://lists.sourceforge.net/lists/listinfo/gmod-ajax > |
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