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From: Keiran R. <kr...@sa...> - 2020-03-07 12:15:18
|
Hi, My slightly biased opinion is cgpBigWig which allows you to generate them per contig and merge into a final file: https://github.com/cancerit/cgpBigWig Docker image is available on Quay.io, and CWL is linked through Dockstore.org. Keiran On 7 Mar 2020 11:56, "Michał T. Lorenc" <m.t...@gm...> wrote: Hi all, I aligned RNA-seq data to a genome and got BAM files. I found here https://jbrowse.org/docs/alignments.html#alignments [jbrowse.org]<https://urldefense.proofpoint.com/v2/url?u=https-3A__jbrowse.org_docs_alignments.html-23alignments&d=DwMFaQ&c=D7ByGjS34AllFgecYw0iC6Zq7qlm8uclZFI0SqQnqBo&r=0l44_2npVb7te0dQGjE0Xw&m=t4HNe2FNA37ek6QEhgQi65Puh1ja5dOfwzFcTyCeWTo&s=z6qb1kqNuozFHsvNSgD0Fiy-tO8xnnrbJoqve_Xenew&e=> that it is possible to create a coverage track for BAM files. Is there any HOWTO to create a coverage track from BAM files and how to load them to JBrowse? Thank you in advance, Michal -- The Wellcome Sanger Institute is operated by Genome Research Limited, a charity registered in England with number 1021457 and a company registered in England with number 2742969, whose registered office is 215 Euston Road, London, NW1 2BE. |
|
From: Michał T. L. <m.t...@gm...> - 2020-03-07 11:56:18
|
Hi all, I aligned RNA-seq data to a genome and got BAM files. I found here https://jbrowse.org/docs/alignments.html#alignments that it is possible to create a coverage track for BAM files. Is there any HOWTO to create a coverage track from BAM files and how to load them to JBrowse? Thank you in advance, Michal |
|
From: Scott C. <sc...@sc...> - 2020-02-21 02:16:33
|
Hello, I am very pleased to announce that GMOD in conjunction with Reactome, Galaxy and OICR/WormBase, together forming Open Genome Informatics, has been accepted for the Google Summer of Code. If you or someone you know might be a student interested in participating in GSoC, please take a look at http://gmod.org/wiki/GSOC_Project_Ideas_2020 where there are proposed projects that cover a fair number of technologies. Official proposals from students will be due in mid March (more on that later). But WAIT! There's more: if you might be interested in being a mentor and working with a student this summer, it's not too late! You can add new project ideas to the page above (contact me if you need an account), or you can even volunteer to add yourself to one of the existing ideas as a potential mentor. Please feel free to forward this to other mailing lists or people who might be interested. We are already an eclectic, dispersed group, so everyone is welcome. Thanks, Scott -- ------------------------------------------------------------------------ Scott Cain, Ph. D. scott at scottcain dot net GMOD Coordinator (http://gmod.org/) 216-392-3087 Ontario Institute for Cancer Research |
|
From: Colin <col...@gm...> - 2020-02-15 00:02:20
|
The mouseover on the track panel uses the HTML title attribute, which is
just a built in browser thing for mouseovers that doesnt allow having HTML
inside it. It would need a fancier mouseover thing to allow HTML in it
You can use track.shortDescription instead of track.metadata.description to
put something in the mouseovers that is not in the About this track popup
-Colin
On Thu, Feb 13, 2020 at 5:26 PM Vaneet Lotay <van...@uc...>
wrote:
> Thank you for the prompt feedback Colin. Yes it’s limited but I think I
> can use those options to work around it.
>
>
>
> This is a somewhat related question. What is the proper way in JBrowse to
> edit the mouseover tooltip that comes up when mousing over the track names
> in the tracklist pane?
>
>
>
> I noticed one method is to fill in a value to the description field within
> metadata like so within a trackList.json file (this would be within a
> specific track stanza):
>
>
>
> ……
>
> “metadata” : {
>
> “Description” : “This is the track description”
>
> },
>
> ……..
>
>
>
> I’ve done this and it takes the place of that mouseover, unfortunately it
> also shows up in the ‘About this track’ box as that same field, so it would
> be nice if there’s a way to simply customize each of those fields
> separately, mainly the mouseover tooltip by itself, is there a way?
>
>
>
> Also I noticed when I place HTML in this mouseover it doesn’t get escaped,
> even if I specify the ‘unsafePopup’ attribute to true. Is there a way to
> make sure any HTML in the mouseover tooltip is not shown as raw HTML and
> gets escaped out?
>
>
>
> Thanks,
>
>
>
> Vaneet
>
>
>
> *From:* Colin <col...@gm...>
> *Sent:* Friday, February 7, 2020 1:03 PM
> *To:* Vaneet Lotay <van...@uc...>
> *Cc:* gmod-ajax <gmo...@li...>
> *Subject:* Re: [Gmod-ajax] JBrowse details box customization
>
>
>
> None of these options are currently available unfortunately. We would
> definitely welcome any pull requests to help perform any of these actions.
> Alternative workarounds could include
>
>
>
> 1) Creating a fully custom view details box to gain custom control over
> how it is displayed
>
> 2) It's not really available to add your own fields to the dialog
> currently, but you could hijack the contents of another field to add some
> custom stuff with the fmtDetailValue callbacks, or again make a fully
> custom view details dialog
>
> 3) A custom view details dialog could be programmed to specially request
> extra sequence data, or again an extensive fmtDetailValue callback could
> potentially be programmed to request upstream/downstream sequence
>
>
>
> Hope that helps (I know it sounds like it's a little limited)
>
>
>
>
>
> -Colin
>
>
>
> On Fri, Feb 7, 2020 at 2:51 PM Vaneet Lotay <van...@uc...>
> wrote:
>
> Hello all,
>
>
>
> I have some questions on what things we are capable of customizing for the
> ‘View details’ pop up box for tracks.
>
>
>
> Currently it appears the attributes under the ‘View details’ box is
> ordered alphabetically for the most part, is there any way to pick a custom
> order for those attributes? I noticed even when I changed the field name
> of one of the attributes, it doesn’t reset the alphabetical order using the
> new field name.
>
>
>
> Is there a way to add your own additional field to ‘View details’ box as
> opposed to just changing the name of a field that’s already there?
>
>
>
> Can I change the coordinates of the Region Sequence in the ‘View details’
> box by including some base pairs upstream or downstream of the region
> sequence and output that in the sequence box instead? Or maybe add an
> additional sequence field with that longer sequence?
>
>
>
> Thanks,
>
>
>
> Vaneet
>
>
>
> *Vaneet Lotay*
>
> *Xenbase Bioinformatician*
>
> *716 ICT Building – University of Calgary*
>
> *2500 University Drive NW*
>
> *Calgary, AB T2N 1N4*
>
> *CANADA*
>
>
>
> _______________________________________________
> Gmod-ajax mailing list
> Gmo...@li...
> https://lists.sourceforge.net/lists/listinfo/gmod-ajax
>
>
|
|
From: Vaneet L. <van...@uc...> - 2020-02-13 22:27:00
|
Thank you for the prompt feedback Colin. Yes it’s limited but I think I can use those options to work around it.
This is a somewhat related question. What is the proper way in JBrowse to edit the mouseover tooltip that comes up when mousing over the track names in the tracklist pane?
I noticed one method is to fill in a value to the description field within metadata like so within a trackList.json file (this would be within a specific track stanza):
……
“metadata” : {
“Description” : “This is the track description”
},
……..
I’ve done this and it takes the place of that mouseover, unfortunately it also shows up in the ‘About this track’ box as that same field, so it would be nice if there’s a way to simply customize each of those fields separately, mainly the mouseover tooltip by itself, is there a way?
Also I noticed when I place HTML in this mouseover it doesn’t get escaped, even if I specify the ‘unsafePopup’ attribute to true. Is there a way to make sure any HTML in the mouseover tooltip is not shown as raw HTML and gets escaped out?
Thanks,
Vaneet
From: Colin <col...@gm...>
Sent: Friday, February 7, 2020 1:03 PM
To: Vaneet Lotay <van...@uc...>
Cc: gmod-ajax <gmo...@li...>
Subject: Re: [Gmod-ajax] JBrowse details box customization
None of these options are currently available unfortunately. We would definitely welcome any pull requests to help perform any of these actions. Alternative workarounds could include
1) Creating a fully custom view details box to gain custom control over how it is displayed
2) It's not really available to add your own fields to the dialog currently, but you could hijack the contents of another field to add some custom stuff with the fmtDetailValue callbacks, or again make a fully custom view details dialog
3) A custom view details dialog could be programmed to specially request extra sequence data, or again an extensive fmtDetailValue callback could potentially be programmed to request upstream/downstream sequence
Hope that helps (I know it sounds like it's a little limited)
-Colin
On Fri, Feb 7, 2020 at 2:51 PM Vaneet Lotay <van...@uc...<mailto:van...@uc...>> wrote:
Hello all,
I have some questions on what things we are capable of customizing for the ‘View details’ pop up box for tracks.
Currently it appears the attributes under the ‘View details’ box is ordered alphabetically for the most part, is there any way to pick a custom order for those attributes? I noticed even when I changed the field name of one of the attributes, it doesn’t reset the alphabetical order using the new field name.
Is there a way to add your own additional field to ‘View details’ box as opposed to just changing the name of a field that’s already there?
Can I change the coordinates of the Region Sequence in the ‘View details’ box by including some base pairs upstream or downstream of the region sequence and output that in the sequence box instead? Or maybe add an additional sequence field with that longer sequence?
Thanks,
Vaneet
Vaneet Lotay
Xenbase Bioinformatician
716 ICT Building – University of Calgary
2500 University Drive NW
Calgary, AB T2N 1N4
CANADA
_______________________________________________
Gmod-ajax mailing list
Gmo...@li...<mailto:Gmo...@li...>
https://lists.sourceforge.net/lists/listinfo/gmod-ajax
|
|
From: Nathan D. <nat...@lb...> - 2020-02-12 16:57:34
|
Samuel, This is more of a Galaxy question specific to the CPT system. I will answer this offline to point you to the right direction. Nathan > On Feb 11, 2020, at 7:11 PM, Munoz, Samuel <sam...@go...> wrote: > > Hello, > > I am a student at Tarleton State University, and we are a part of the sea-PHAGES program. > > This is our first-time using Galaxy so we are still figuring things out, but we are having issues. We want to be able to share one history/workflow so that all the classmates can work on the same file. Currently, we are having issues with this. We are able to share the history but when we open the page on Apollo, it shows completely different information. We are unsure on how to fix this issue or if we missed a step. > > Basically, we want to be able to use one workflow/history between all the classmates so that we are able to quickly edit the information, and everyone have access to that updated information. > > Thank you > > Samuel Munoz > > > > _______________________________________________ > Gmod-ajax mailing list > Gmo...@li... <mailto:Gmo...@li...> > https://lists.sourceforge.net/lists/listinfo/gmod-ajax <https://lists.sourceforge.net/lists/listinfo/gmod-ajax> |
|
From: Nathan D. <nat...@lb...> - 2020-02-12 16:56:31
|
Gustavo, I think this is more of a specific Galaxy question for the server you are on. I am answering separately offline. Nathan > On Feb 11, 2020, at 7:13 PM, Vazquez, Gustavo <gus...@go...> wrote: > > Hello, > > My name is Gustavo Vazquez. I am a student at Tarleton State University and currently in the Phage Discovery Program. As a class, we been using Galaxy/CPT Public to edit and determine the genes of a genome, but we encounter a problem. We cannot collaborate as a group, meaning that each students work does not show up on another student’s galaxy/ CPT public data. I believe this is due to working on separate desktop, but is there a way we can all collaborate to edit the genes from different desktops? > > Sincerely, Gustavo vazquez > _______________________________________________ > Gmod-ajax mailing list > Gmo...@li... <mailto:Gmo...@li...> > https://lists.sourceforge.net/lists/listinfo/gmod-ajax <https://lists.sourceforge.net/lists/listinfo/gmod-ajax> |
|
From: Munoz, S. <sam...@go...> - 2020-02-12 04:44:59
|
Hello, I am a student at Tarleton State University, and we are a part of the sea-PHAGES program. This is our first-time using Galaxy so we are still figuring things out, but we are having issues. We want to be able to share one history/workflow so that all the classmates can work on the same file. Currently, we are having issues with this. We are able to share the history but when we open the page on Apollo, it shows completely different information. We are unsure on how to fix this issue or if we missed a step. Basically, we want to be able to use one workflow/history between all the classmates so that we are able to quickly edit the information, and everyone have access to that updated information. Thank you Samuel Munoz |
|
From: Vazquez, G. <gus...@go...> - 2020-02-12 03:47:42
|
Hello, My name is Gustavo Vazquez. I am a student at Tarleton State University and currently in the Phage Discovery Program. As a class, we been using Galaxy/CPT Public to edit and determine the genes of a genome, but we encounter a problem. We cannot collaborate as a group, meaning that each students work does not show up on another student’s galaxy/ CPT public data. I believe this is due to working on separate desktop, but is there a way we can all collaborate to edit the genes from different desktops? Sincerely, Gustavo vazquez |
|
From: Pengcheng Y. <pen...@qq...> - 2020-02-12 02:04:21
|
Hi Colin and Robert, After convert the bam to cram, it has been successfully displayed (http://insectmine.org/jbrowse/index.html?data=FAWMine). Thank you all! best, Pengcheng On 2020-2-12 4:48, Robert Buels wrote: > Another common Apache module that causes this is mod_mime_magic, so > make sure that's not operating on these files either, if you are > indeed running an Apache server > > On Tue, Feb 11, 2020 at 8:48 AM Colin <col...@gm... > <mailto:col...@gm...>> wrote: > > I can see from the Chrome Devtools that the range requests for the > BAM file produce this error > > net::ERR_CONTENT_DECODING_FAILED > > "This can happen when an HTTP request's headers claim that the > content is gzip encoded" > > https://superuser.com/questions/172951/chrome-error-330-neterr-content-decoding-failed > > Doing curl of the file shows that the response has this on the > response > > Content-Encoding: x-gzip > > Basically you do not want this header on your response. Some > common things include having mod_deflate on the server, but it's > hard to know exactly what server side conditions caused this > > > -Colin > > On Tue, Feb 11, 2020 at 11:44 AM Pengcheng Yang <pen...@qq... > <mailto:pen...@qq...>> wrote: > > Hi Colin, > > I have just checked the Network tab in the chrome devtools and > full screen shot is shown below. Please help me check how > could I resolve this problem. > > > Thank you and best, > > pengcheng > > On 2020-2-11 23:17, Colin wrote: >> Could you look at the network tab in the chrome devtools and >> see if there are any indicators of what the network request >> says? Maybe paste a full screenshot of the network tab? >> >> The server itself will never produce "HTTP status that is >> undefined" but sometimes things in the middle e.g. firewall >> or decoding of the request can cause HTTP status to be 0 or >> undefined >> >> An example may be gzip related, as the browser might receive >> a bad response containing the wrong gzip headers, then try to >> ungzip the data, and then maybe fail >> >> -Colin >> >> On Tue, Feb 11, 2020 at 6:32 AM Pengcheng Yang >> <pen...@qq... <mailto:pen...@qq...>> wrote: >> >> Dear JBrowsers: >> >> I am trying loading BAM file as the documentation >> suggested. However, I am failed with the error message >> said "Error: HTTP undefined when fetching http://...." >> >> >> The json configuration information is: >> >> { >> "category": "RNA-Seq", >> "key" : "TR2010b", >> "label": "TR2010b", >> "storeClass" : "JBrowse/Store/SeqFeature/BAM", >> "type" : "JBrowse/View/Track/Alignments2", >> "urlTemplate": "BAM/TR2012b.fa.map.bam", >> "baiUrlTemplate" : "BAM/TR2012b.fa.map.bam.bai" >> } >> >> Could anyone help me out? >> >> Thank you and best, >> >> Pengcheng Yang >> >> >> _______________________________________________ >> Gmod-ajax mailing list >> Gmo...@li... >> <mailto:Gmo...@li...> >> https://lists.sourceforge.net/lists/listinfo/gmod-ajax >> > _______________________________________________ > Gmod-ajax mailing list > Gmo...@li... > <mailto:Gmo...@li...> > https://lists.sourceforge.net/lists/listinfo/gmod-ajax > |
|
From: Robert B. <rb...@gm...> - 2020-02-11 20:49:08
|
Another common Apache module that causes this is mod_mime_magic, so make sure that's not operating on these files either, if you are indeed running an Apache server On Tue, Feb 11, 2020 at 8:48 AM Colin <col...@gm...> wrote: > I can see from the Chrome Devtools that the range requests for the BAM > file produce this error > > net::ERR_CONTENT_DECODING_FAILED > > "This can happen when an HTTP request's headers claim that the content is > gzip encoded" > > > https://superuser.com/questions/172951/chrome-error-330-neterr-content-decoding-failed > > Doing curl of the file shows that the response has this on the response > > Content-Encoding: x-gzip > > Basically you do not want this header on your response. Some common things > include having mod_deflate on the server, but it's hard to know exactly > what server side conditions caused this > > > -Colin > > On Tue, Feb 11, 2020 at 11:44 AM Pengcheng Yang <pen...@qq...> wrote: > >> Hi Colin, >> >> I have just checked the Network tab in the chrome devtools and full >> screen shot is shown below. Please help me check how could I resolve this >> problem. >> >> >> Thank you and best, >> >> pengcheng >> On 2020-2-11 23:17, Colin wrote: >> >> Could you look at the network tab in the chrome devtools and see if there >> are any indicators of what the network request says? Maybe paste a full >> screenshot of the network tab? >> >> The server itself will never produce "HTTP status that is undefined" but >> sometimes things in the middle e.g. firewall or decoding of the request can >> cause HTTP status to be 0 or undefined >> >> An example may be gzip related, as the browser might receive a bad >> response containing the wrong gzip headers, then try to ungzip the data, >> and then maybe fail >> >> -Colin >> >> On Tue, Feb 11, 2020 at 6:32 AM Pengcheng Yang <pen...@qq...> wrote: >> >>> Dear JBrowsers: >>> >>> I am trying loading BAM file as the documentation suggested. However, I >>> am failed with the error message said "Error: HTTP undefined when fetching >>> http://...." >>> >>> >>> The json configuration information is: >>> >>> { >>> "category": "RNA-Seq", >>> "key" : "TR2010b", >>> "label": "TR2010b", >>> "storeClass" : "JBrowse/Store/SeqFeature/BAM", >>> "type" : "JBrowse/View/Track/Alignments2", >>> "urlTemplate": "BAM/TR2012b.fa.map.bam", >>> "baiUrlTemplate" : "BAM/TR2012b.fa.map.bam.bai" >>> } >>> >>> Could anyone help me out? >>> >>> Thank you and best, >>> >>> Pengcheng Yang >>> >>> >>> _______________________________________________ >>> 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 > |
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From: Nathan D. <nat...@lb...> - 2020-02-11 19:30:33
|
There are many amazing topics there as usual. Of note for our communities: - JBrowse 2 (JB2) embedding - writing JB2 plugins - using Apollo and Maker within Galaxy for genome assembly and annotation Hope to see some of you there! Nathan > On Feb 11, 2020, at 9:29 AM, Nathan Dunn <nat...@lb...> wrote: > > > BOSC + Galaxy in Toronto this summer. > > Please vote on topics if attending! > > Nathan > > >> Begin forwarded message: >> >> From: Dave Clements <cle...@gm... <mailto:cle...@gm...>> >> Subject: [Gmod-announce] BCC2020 Training Topic Voting is Open >> Date: February 11, 2020 at 6:35:00 AM PST >> To: Galaxy Announcements List <gal...@li... <mailto:gal...@li...>>, Galaxy Dev List <gal...@li... <mailto:gal...@li...>>, BOSC Announce <bos...@go... <mailto:bos...@go...>>, GMOD Announcements List <gmo...@li... <mailto:gmo...@li...>>, GMOD Developers List <gmo...@li... <mailto:gmo...@li...>>, BCC2020 Interest <bcc...@li... <mailto:bcc...@li...>> >> Cc: BCC2020 Organizers <bcc...@li... <mailto:bcc...@li...>> >> >> Hello all, >> >> The The Bioinformatics Community Conference (BCC2020) <https://bcc2020.github.io/>, will bring together the Galaxy Community Conference (GCC) and the Bioinformatics Open Source Conference (BOSC) in Toronto, Canada in July 2020, following ISMB 2020 <https://www.iscb.org/ismb2020> in Montréal. BCC2020 will start with a dedicated training day, followed by 3 days of mixed meeting and training events. >> >> The community (you!) determines what training will be offered at BCC2020. Nominations from the community <https://bcc2020.github.io/training/> are now ready for review and voting. If you are possibly attending BCC2020 then please take a few minutes to review the nominations and then submit your ballot <https://docs.google.com/forms/d/e/1FAIpQLSfmOowsHt0cL1ukiGvOdh7WxWKoSuT-3GMnUFGQGvmarxlzQg/viewform>. Voting closes on February 21. >> >> Thanks in advance for your input, and we hope to see you in Toronto, >> BCC2020 Organizers >> >> -- >> https://galaxyproject.org/ <https://galaxyproject.org/> >> _______________________________________________ >> Gmod-announce mailing list >> Gmo...@li... <mailto:Gmo...@li...> >> https://lists.sourceforge.net/lists/listinfo/gmod-announce > |
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From: Nathan D. <nat...@lb...> - 2020-02-11 17:32:30
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BOSC + Galaxy in Toronto this summer. Please vote on topics if attending! Nathan > Begin forwarded message: > > From: Dave Clements <cle...@gm...> > Subject: [Gmod-announce] BCC2020 Training Topic Voting is Open > Date: February 11, 2020 at 6:35:00 AM PST > To: Galaxy Announcements List <gal...@li...>, Galaxy Dev List <gal...@li...>, BOSC Announce <bos...@go...>, GMOD Announcements List <gmo...@li...>, GMOD Developers List <gmo...@li...>, BCC2020 Interest <bcc...@li...> > Cc: BCC2020 Organizers <bcc...@li...> > > Hello all, > > The The Bioinformatics Community Conference (BCC2020) <https://bcc2020.github.io/>, will bring together the Galaxy Community Conference (GCC) and the Bioinformatics Open Source Conference (BOSC) in Toronto, Canada in July 2020, following ISMB 2020 <https://www.iscb.org/ismb2020> in Montréal. BCC2020 will start with a dedicated training day, followed by 3 days of mixed meeting and training events. > > The community (you!) determines what training will be offered at BCC2020. Nominations from the community <https://bcc2020.github.io/training/> are now ready for review and voting. If you are possibly attending BCC2020 then please take a few minutes to review the nominations and then submit your ballot <https://docs.google.com/forms/d/e/1FAIpQLSfmOowsHt0cL1ukiGvOdh7WxWKoSuT-3GMnUFGQGvmarxlzQg/viewform>. Voting closes on February 21. > > Thanks in advance for your input, and we hope to see you in Toronto, > BCC2020 Organizers > > -- > https://galaxyproject.org/ <https://galaxyproject.org/> > _______________________________________________ > Gmod-announce mailing list > Gmo...@li... > https://lists.sourceforge.net/lists/listinfo/gmod-announce |
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From: Colin <col...@gm...> - 2020-02-11 16:47:58
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I can see from the Chrome Devtools that the range requests for the BAM file produce this error net::ERR_CONTENT_DECODING_FAILED "This can happen when an HTTP request's headers claim that the content is gzip encoded" https://superuser.com/questions/172951/chrome-error-330-neterr-content-decoding-failed Doing curl of the file shows that the response has this on the response Content-Encoding: x-gzip Basically you do not want this header on your response. Some common things include having mod_deflate on the server, but it's hard to know exactly what server side conditions caused this -Colin On Tue, Feb 11, 2020 at 11:44 AM Pengcheng Yang <pen...@qq...> wrote: > Hi Colin, > > I have just checked the Network tab in the chrome devtools and full screen > shot is shown below. Please help me check how could I resolve this problem. > > > Thank you and best, > > pengcheng > On 2020-2-11 23:17, Colin wrote: > > Could you look at the network tab in the chrome devtools and see if there > are any indicators of what the network request says? Maybe paste a full > screenshot of the network tab? > > The server itself will never produce "HTTP status that is undefined" but > sometimes things in the middle e.g. firewall or decoding of the request can > cause HTTP status to be 0 or undefined > > An example may be gzip related, as the browser might receive a bad > response containing the wrong gzip headers, then try to ungzip the data, > and then maybe fail > > -Colin > > On Tue, Feb 11, 2020 at 6:32 AM Pengcheng Yang <pen...@qq...> wrote: > >> Dear JBrowsers: >> >> I am trying loading BAM file as the documentation suggested. However, I >> am failed with the error message said "Error: HTTP undefined when fetching >> http://...." >> >> >> The json configuration information is: >> >> { >> "category": "RNA-Seq", >> "key" : "TR2010b", >> "label": "TR2010b", >> "storeClass" : "JBrowse/Store/SeqFeature/BAM", >> "type" : "JBrowse/View/Track/Alignments2", >> "urlTemplate": "BAM/TR2012b.fa.map.bam", >> "baiUrlTemplate" : "BAM/TR2012b.fa.map.bam.bai" >> } >> >> Could anyone help me out? >> >> Thank you and best, >> >> Pengcheng Yang >> >> >> _______________________________________________ >> Gmod-ajax mailing list >> Gmo...@li... >> https://lists.sourceforge.net/lists/listinfo/gmod-ajax >> > |
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From: Nathan D. <nat...@lb...> - 2020-02-11 16:46:25
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From Helena Rasche of the Galaxy (and often Apollo and other GMOD) communities. ==== Hi Apollo community! I'm part of a group applying for a grant (Erasmus+) for providing training in Europe, we're going to have a Genome Annotation (Galaxy + MAKER/Prokka + Apollo) training track so naturally we're looking for groups that might be interested in joining these training events. If your group is in the EU and is doing genome annotation/apollo/interested in helping build the genome annotation community locally, please let me know. Cheers, Helena The background, for those interested: Last year we piloted distributed training <https://galaxy-carpentries.github.io/gallantries/>, where we got some of the best Galaxy trainers in HTS to teach that topic, and then we broadcast them across Europe. Interested groups simply announced a workshop, ordered some coffee and booked a computer room, and then joined the live stream. The training, Galaxy administration, Galaxy compute resources, everything else was handled for them. This new way of doing training lets us scale dramatically; instead of having the best person teach 20 students at one time, we can enable them to teach 200 across 10 sites! And all without the cost of lodging, travel, or the CO2 emitted during travel. This year we’re applying for a grant which will enable us to scale this idea further, and we’re adding three new tracks to the distributed training: Ecology, Metagenomics, and Genome Annotation. |
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From: Pengcheng Y. <pen...@qq...> - 2020-02-11 16:44:45
|
Hi Colin,
I have just checked the Network tab in the chrome devtools and full
screen shot is shown below. Please help me check how could I resolve
this problem.
Thank you and best,
pengcheng
On 2020-2-11 23:17, Colin wrote:
> Could you look at the network tab in the chrome devtools and see if
> there are any indicators of what the network request says? Maybe
> paste a full screenshot of the network tab?
>
> The server itself will never produce "HTTP status that is undefined"
> but sometimes things in the middle e.g. firewall or decoding of the
> request can cause HTTP status to be 0 or undefined
>
> An example may be gzip related, as the browser might receive a bad
> response containing the wrong gzip headers, then try to ungzip the
> data, and then maybe fail
>
> -Colin
>
> On Tue, Feb 11, 2020 at 6:32 AM Pengcheng Yang <pen...@qq...
> <mailto:pen...@qq...>> wrote:
>
> Dear JBrowsers:
>
> I am trying loading BAM file as the documentation suggested.
> However, I am failed with the error message said "Error: HTTP
> undefined when fetching http://...."
>
>
> The json configuration information is:
>
> {
> "category": "RNA-Seq",
> "key" : "TR2010b",
> "label": "TR2010b",
> "storeClass" : "JBrowse/Store/SeqFeature/BAM",
> "type" : "JBrowse/View/Track/Alignments2",
> "urlTemplate": "BAM/TR2012b.fa.map.bam",
> "baiUrlTemplate" : "BAM/TR2012b.fa.map.bam.bai"
> }
>
> Could anyone help me out?
>
> Thank you and best,
>
> Pengcheng Yang
>
>
> _______________________________________________
> Gmod-ajax mailing list
> Gmo...@li...
> <mailto:Gmo...@li...>
> https://lists.sourceforge.net/lists/listinfo/gmod-ajax
>
|
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From: Pengcheng Y. <pen...@qq...> - 2020-02-11 16:35:29
|
Hi Colin, Thank you for your reply. The web address of the jbrowse is: http://insectmine.org/jbrowse/index.html?data=FAWMine, please test if you can get the same error as mine. The following picture is the full screen of the jbrowse webpage. best, Pengcheng On 2020-2-11 23:17, Colin wrote: > Could you look at the network tab in the chrome devtools and see if > there are any indicators of what the network request says? Maybe > paste a full screenshot of the network tab? > > The server itself will never produce "HTTP status that is undefined" > but sometimes things in the middle e.g. firewall or decoding of the > request can cause HTTP status to be 0 or undefined > > An example may be gzip related, as the browser might receive a bad > response containing the wrong gzip headers, then try to ungzip the > data, and then maybe fail > > -Colin > > On Tue, Feb 11, 2020 at 6:32 AM Pengcheng Yang <pen...@qq... > <mailto:pen...@qq...>> wrote: > > Dear JBrowsers: > > I am trying loading BAM file as the documentation suggested. > However, I am failed with the error message said "Error: HTTP > undefined when fetching http://...." > > > The json configuration information is: > > { > "category": "RNA-Seq", > "key" : "TR2010b", > "label": "TR2010b", > "storeClass" : "JBrowse/Store/SeqFeature/BAM", > "type" : "JBrowse/View/Track/Alignments2", > "urlTemplate": "BAM/TR2012b.fa.map.bam", > "baiUrlTemplate" : "BAM/TR2012b.fa.map.bam.bai" > } > > Could anyone help me out? > > Thank you and best, > > Pengcheng Yang > > > _______________________________________________ > Gmod-ajax mailing list > Gmo...@li... > <mailto:Gmo...@li...> > https://lists.sourceforge.net/lists/listinfo/gmod-ajax > |
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From: Colin <col...@gm...> - 2020-02-11 15:18:18
|
Could you look at the network tab in the chrome devtools and see if there
are any indicators of what the network request says? Maybe paste a full
screenshot of the network tab?
The server itself will never produce "HTTP status that is undefined" but
sometimes things in the middle e.g. firewall or decoding of the request can
cause HTTP status to be 0 or undefined
An example may be gzip related, as the browser might receive a bad response
containing the wrong gzip headers, then try to ungzip the data, and then
maybe fail
-Colin
On Tue, Feb 11, 2020 at 6:32 AM Pengcheng Yang <pen...@qq...> wrote:
> Dear JBrowsers:
>
> I am trying loading BAM file as the documentation suggested. However, I am
> failed with the error message said "Error: HTTP undefined when fetching
> http://...."
>
>
> The json configuration information is:
>
> {
> "category": "RNA-Seq",
> "key" : "TR2010b",
> "label": "TR2010b",
> "storeClass" : "JBrowse/Store/SeqFeature/BAM",
> "type" : "JBrowse/View/Track/Alignments2",
> "urlTemplate": "BAM/TR2012b.fa.map.bam",
> "baiUrlTemplate" : "BAM/TR2012b.fa.map.bam.bai"
> }
>
> Could anyone help me out?
>
> Thank you and best,
>
> Pengcheng Yang
>
>
> _______________________________________________
> Gmod-ajax mailing list
> Gmo...@li...
> https://lists.sourceforge.net/lists/listinfo/gmod-ajax
>
|
|
From: Pengcheng Y. <pen...@qq...> - 2020-02-11 11:32:17
|
Dear JBrowsers:
I am trying loading BAM file as the documentation suggested. However, I
am failed with the error message said "Error: HTTP undefined when
fetching http://...."
The json configuration information is:
{
"category": "RNA-Seq",
"key" : "TR2010b",
"label": "TR2010b",
"storeClass" : "JBrowse/Store/SeqFeature/BAM",
"type" : "JBrowse/View/Track/Alignments2",
"urlTemplate": "BAM/TR2012b.fa.map.bam",
"baiUrlTemplate" : "BAM/TR2012b.fa.map.bam.bai"
}
Could anyone help me out?
Thank you and best,
Pengcheng Yang
|
|
From: Colin <col...@gm...> - 2020-02-07 20:02:52
|
None of these options are currently available unfortunately. We would definitely welcome any pull requests to help perform any of these actions. Alternative workarounds could include 1) Creating a fully custom view details box to gain custom control over how it is displayed 2) It's not really available to add your own fields to the dialog currently, but you could hijack the contents of another field to add some custom stuff with the fmtDetailValue callbacks, or again make a fully custom view details dialog 3) A custom view details dialog could be programmed to specially request extra sequence data, or again an extensive fmtDetailValue callback could potentially be programmed to request upstream/downstream sequence Hope that helps (I know it sounds like it's a little limited) -Colin On Fri, Feb 7, 2020 at 2:51 PM Vaneet Lotay <van...@uc...> wrote: > Hello all, > > > > I have some questions on what things we are capable of customizing for the > ‘View details’ pop up box for tracks. > > > > Currently it appears the attributes under the ‘View details’ box is > ordered alphabetically for the most part, is there any way to pick a custom > order for those attributes? I noticed even when I changed the field name > of one of the attributes, it doesn’t reset the alphabetical order using the > new field name. > > > > Is there a way to add your own additional field to ‘View details’ box as > opposed to just changing the name of a field that’s already there? > > > > Can I change the coordinates of the Region Sequence in the ‘View details’ > box by including some base pairs upstream or downstream of the region > sequence and output that in the sequence box instead? Or maybe add an > additional sequence field with that longer sequence? > > > > Thanks, > > > > Vaneet > > > > *Vaneet Lotay* > > *Xenbase Bioinformatician* > > *716 ICT Building – University of Calgary* > > *2500 University Drive NW* > > *Calgary, AB T2N 1N4* > > *CANADA* > > > _______________________________________________ > Gmod-ajax mailing list > Gmo...@li... > https://lists.sourceforge.net/lists/listinfo/gmod-ajax > |
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From: Vaneet L. <van...@uc...> - 2020-02-07 19:50:55
|
Hello all, I have some questions on what things we are capable of customizing for the 'View details' pop up box for tracks. Currently it appears the attributes under the 'View details' box is ordered alphabetically for the most part, is there any way to pick a custom order for those attributes? I noticed even when I changed the field name of one of the attributes, it doesn't reset the alphabetical order using the new field name. Is there a way to add your own additional field to 'View details' box as opposed to just changing the name of a field that's already there? Can I change the coordinates of the Region Sequence in the 'View details' box by including some base pairs upstream or downstream of the region sequence and output that in the sequence box instead? Or maybe add an additional sequence field with that longer sequence? Thanks, Vaneet Vaneet Lotay Xenbase Bioinformatician 716 ICT Building - University of Calgary 2500 University Drive NW Calgary, AB T2N 1N4 CANADA |
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From: Colin <col...@gm...> - 2020-02-05 03:00:47
|
Hi all, This JBrowse release addresses a bug in JBrowse 1.16.7 when using GFF3Tabix. The features were being corrupted around bgzip block boundaries. Please upgrade if you get a chance and let us know if you see any further issues. Thanks! - JBrowse-1.16.8.zip <https://github.com/GMOD/jbrowse/releases/download/1.16.8-release/JBrowse-1.16.8.zip> - minified release - JBrowse-1.16.8-dev.zip <https://github.com/GMOD/jbrowse/archive/1.16.8-release.zip> - use this if you modify jbrowse source code or use plugins - JBrowse-1.16.8-desktop-win32-x64.zip <https://github.com/GMOD/jbrowse/releases/download/1.16.8-release/JBrowse-1.16.8-desktop-win32-x64.zip> - JBrowse-1.16.8-desktop-linux-x64.zip <https://github.com/GMOD/jbrowse/releases/download/1.16.8-release/JBrowse-1.16.8-desktop-linux-x64.zip> - JBrowse-1.16.8-desktop-darwin-x64.zip <https://github.com/GMOD/jbrowse/releases/download/1.16.8-release/JBrowse-1.16.8-desktop-darwin-x64.zip> Bug fixes - Fixed an regression that made corrupted features around bgzip block boundaries. Related to @gmod <https://github.com/gmod>/tabix 1.2.0->1.3.2 fileOffset based feature ID. Bug affected JBrowse 1.16.7 (issue #1464 <https://github.com/gmod/jbrowse/issues/1464>) |
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From: Colin <col...@gm...> - 2020-02-02 16:35:16
|
This command might appear if your gff3 is not tab separated columns e.g. there are spaces instead of tabs Can you check that the gff is tab separated? -Colin On Sun, Feb 2, 2020 at 11:32 AM Michał T. Lorenc <m.t...@gm...> wrote: > Hi all, > After the running the below command I got *WARNING: No matching features > found for mRNA *and the track is empty: > > > *$ perl ~/tomcat7-deploy/apollo/jbrowse/bin/flatfile-to-json.pl > <http://flatfile-to-json.pl> --nameAttributes "ID,Name,Note" --gff > /efs/apollo/QUT > NbRNASeqAll.sorted-proper.add-rg.bam.dedup.bam.gtf.fasta.transdecoder.genome.FixVSaugustus.hints_utrAGAT.newID-swissprot.filtered.gff3 > --compress --trackType HTMLFeatures --trackLabel > "NbRNASeqAll.sorted-proper.add-rg.bam.dedup.bam.gtf.fasta.transdecoder.genome.FixVSaugustus.hints_utrAGAT.newID-swissprot.filtered" > --type=mRNA --out /efs/apollo/QUTWARNING: No matching features found for > mRNA* > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > *$ head -n 100 > NbRNASeqAll.sorted-proper.add-rg.bam.dedup.bam.gtf.fasta.transdecoder.genome.FixVSaugustus.hints_utrAGAT.newID-swissprot.filtered.gff3##gff-version > 3##sequence-region NbV1Ch01 1 187320599NbV1Ch01 transdecoder gene 98185 > 99705 . - . ID=NBlab01G00010NbV1Ch01 transdecoder mRNA 98185 99705 . - . > ID=NBlab01G00010.1;Note=Peroxidase 40;Parent=NBlab01G00010NbV1Ch01 > transdecoder exon 98185 98571 . - . > ID=NBlab01G00010.1.exon4;Parent=NBlab01G00010.1NbV1Ch01 transdecoder exon > 98679 98844 . - . ID=NBlab01G00010.1.exon3;Parent=NBlab01G00010.1NbV1Ch01 > transdecoder exon 99134 99325 . - . > ID=NBlab01G00010.1.exon2;Parent=NBlab01G00010.1NbV1Ch01 transdecoder exon > 99417 99705 . - . ID=NBlab01G00010.1.exon1;Parent=NBlab01G00010.1NbV1Ch01 > transdecoder CDS 98186 98571 . - 2 > ID=NBlab01G00010.1.cds;Parent=NBlab01G00010.1NbV1Ch01 transdecoder CDS > 98679 98844 . - 0 ID=NBlab01G00010.1.cds;Parent=NBlab01G00010.1NbV1Ch01 > transdecoder CDS 99134 99325 . - 0 > ID=NBlab01G00010.1.cds;Parent=NBlab01G00010.1NbV1Ch01 transdecoder CDS > 99417 99704 . - 0 ID=NBlab01G00010.1.cds;Parent=NBlab01G00010.1NbV1Ch01 > transdecoder five_prime_UTR 99705 99705 . - . > ID=NBlab01G00010.1.5UTRg1;Parent=NBlab01G00010.1NbV1Ch01 transdecoder > three_prime_UTR 98185 98185 . - . > ID=NBlab01G00010.1.3UTRg1;Parent=NBlab01G00010.1NbV1Ch01 transdecoder gene > 212254 223251 . - . ID=NBlab01G00060NbV1Ch01 transdecoder mRNA 212254 > 223251 . - . ID=NBlab01G00060.1;Note=P34 probable thiol > protease;Parent=NBlab01G00060NbV1Ch01 transdecoder exon 212254 212731 . - . > ID=NBlab01G00060.1.exon5;Parent=NBlab01G00060.1NbV1Ch01 transdecoder exon > 212829 212968 . - . ID=NBlab01G00060.1.exon4;Parent=NBlab01G00060.1NbV1Ch01 > transdecoder exon 218080 219546 . - . > ID=NBlab01G00060.1.exon3;Parent=NBlab01G00060.1NbV1Ch01 transdecoder exon > 219642 222881 . - . ID=NBlab01G00060.1.exon2;Parent=NBlab01G00060.1NbV1Ch01 > transdecoder exon 222989 223251 . - . > ID=NBlab01G00060.1.exon1;Parent=NBlab01G00060.1NbV1Ch01 transdecoder CDS > 219287 219546 . - 2 ID=NBlab01G00060.1.cds;Parent=NBlab01G00060.1NbV1Ch01 > transdecoder CDS 219642 219711 . - 0 > ID=NBlab01G00060.1.cds;Parent=NBlab01G00060.1NbV1Ch01 transdecoder > five_prime_UTR 219712 222881 . - . > ID=NBlab01G00060.1.utr5p2;Parent=NBlab01G00060.1NbV1Ch01 transdecoder > five_prime_UTR 222989 223251 . - . > ID=NBlab01G00060.1.utr5p1;Parent=NBlab01G00060.1NbV1Ch01 transdecoder > three_prime_UTR 212254 212731 . - . > ID=NBlab01G00060.1.utr3p3;Parent=NBlab01G00060.1NbV1Ch01 transdecoder > three_prime_UTR 212829 212968 . - . > ID=NBlab01G00060.1.utr3p2;Parent=NBlab01G00060.1NbV1Ch01 transdecoder > three_prime_UTR 218080 219286 . - . > ID=NBlab01G00060.1.utr3p1;Parent=NBlab01G00060.1NbV1Ch01 transdecoder mRNA > 212254 223251 . - . ID=NBlab01G00060.2;Note=Cysteine proteinase COT44 > %28Fragment%29;Parent=NBlab01G00060NbV1Ch01 transdecoder exon 212254 212731 > . - . ID=NBlab01G00060.2.exon8;Parent=NBlab01G00060.2NbV1Ch01 transdecoder > exon 212829 212968 . - . > ID=NBlab01G00060.2.exon7;Parent=NBlab01G00060.2NbV1Ch01 transdecoder exon > 218080 218969 . - . ID=NBlab01G00060.2.exon6;Parent=NBlab01G00060.2NbV1Ch01 > transdecoder exon 219061 219198 . - . > ID=NBlab01G00060.2.exon5;Parent=NBlab01G00060.2NbV1Ch01 transdecoder exon > 219271 219546 . - . ID=NBlab01G00060.2.exon4;Parent=NBlab01G00060.2NbV1Ch01 > transdecoder exon 219642 219702 . - . > ID=NBlab01G00060.2.exon3;Parent=NBlab01G00060.2NbV1Ch01 transdecoder exon > 219814 222881 . - . ID=NBlab01G00060.2.exon2;Parent=NBlab01G00060.2NbV1Ch01 > transdecoder exon 222989 223251 . - . > ID=NBlab01G00060.2.exon1;Parent=NBlab01G00060.2NbV1Ch01 transdecoder CDS > 218733 218969 . - 0 ID=NBlab01G00060.2.cds;Parent=NBlab01G00060.2NbV1Ch01 > transdecoder CDS 219061 219198 . - 0 > ID=NBlab01G00060.2.cds;Parent=NBlab01G00060.2NbV1Ch01 transdecoder CDS > 219271 219345 . - 0 ID=NBlab01G00060.2.cds;Parent=NBlab01G00060.2NbV1Ch01 > transdecoder five_prime_UTR 219346 219546 . - . > ID=NBlab01G00060.2.utr5p4;Parent=NBlab01G00060.2NbV1Ch01 transdecoder > five_prime_UTR 219642 219702 . - . > ID=NBlab01G00060.2.utr5p3;Parent=NBlab01G00060.2NbV1Ch01 transdecoder > five_prime_UTR 219814 222881 . - . > ID=NBlab01G00060.2.utr5p2;Parent=NBlab01G00060.2NbV1Ch01 transdecoder > five_prime_UTR 222989 223251 . - . > ID=NBlab01G00060.2.utr5p1;Parent=NBlab01G00060.2NbV1Ch01 transdecoder > three_prime_UTR 212254 212731 . - . > ID=NBlab01G00060.2.utr3p3;Parent=NBlab01G00060.2NbV1Ch01 transdecoder > three_prime_UTR 212829 212968 . - . > ID=NBlab01G00060.2.utr3p2;Parent=NBlab01G00060.2NbV1Ch01 transdecoder > three_prime_UTR 218080 218732 . - . > ID=NBlab01G00060.2.utr3p1;Parent=NBlab01G00060.2NbV1Ch01 transdecoder mRNA > 212254 223251 . - . ID=NBlab01G00060.3;Note=P34 probable thiol > protease;Parent=NBlab01G00060NbV1Ch01 transdecoder exon 212254 212731 . - . > ID=NBlab01G00060.3.exon7;Parent=NBlab01G00060.3NbV1Ch01 transdecoder exon > 212829 212968 . - . ID=NBlab01G00060.3.exon6;Parent=NBlab01G00060.3NbV1Ch01 > transdecoder exon 218080 218386 . - . > ID=NBlab01G00060.3.exon5;Parent=NBlab01G00060.3NbV1Ch01 transdecoder exon > 219061 219546 . - . ID=NBlab01G00060.3.exon4;Parent=NBlab01G00060.3NbV1Ch01 > transdecoder exon 219642 219702 . - . > ID=NBlab01G00060.3.exon3;Parent=NBlab01G00060.3NbV1Ch01 transdecoder exon > 219866 222881 . - . ID=NBlab01G00060.3.exon2;Parent=NBlab01G00060.3NbV1Ch01 > transdecoder exon 222989 223251 . - . > ID=NBlab01G00060.3.exon1;Parent=NBlab01G00060.3NbV1Ch01 transdecoder CDS > 219287 219546 . - 2 ID=NBlab01G00060.3.cds;Parent=NBlab01G00060.3NbV1Ch01 > transdecoder CDS 219642 219702 . - 0 > ID=NBlab01G00060.3.cds;Parent=NBlab01G00060.3NbV1Ch01 transdecoder CDS > 219866 219940 . - 0 ID=NBlab01G00060.3.cds;Parent=NBlab01G00060.3NbV1Ch01 > transdecoder five_prime_UTR 219941 222881 . - . > ID=NBlab01G00060.3.utr5p2;Parent=NBlab01G00060.3NbV1Ch01 transdecoder > five_prime_UTR 222989 223251 . - . > ID=NBlab01G00060.3.utr5p1;Parent=NBlab01G00060.3NbV1Ch01 transdecoder > three_prime_UTR 212254 212731 . - . > ID=NBlab01G00060.3.utr3p4;Parent=NBlab01G00060.3NbV1Ch01 transdecoder > three_prime_UTR 212829 212968 . - . > ID=NBlab01G00060.3.utr3p3;Parent=NBlab01G00060.3NbV1Ch01 transdecoder > three_prime_UTR 218080 218386 . - . > ID=NBlab01G00060.3.utr3p2;Parent=NBlab01G00060.3NbV1Ch01 transdecoder > three_prime_UTR 219061 219286 . - . > ID=NBlab01G00060.3.utr3p1;Parent=NBlab01G00060.3NbV1Ch01 AUGUSTUS gene > 220636 222022 0.53 + . ID=NBlab01G00070NbV1Ch01 AUGUSTUS mRNA 220636 222022 > 0.1 + . ID=NBlab01G00070.2;Note=P34 probable thiol > protease;Parent=NBlab01G00070NbV1Ch01 AUGUSTUS exon 220636 221012 . + . > ID=NBlab01G00070.2.exon1;Parent=NBlab01G00070.2NbV1Ch01 AUGUSTUS exon > 221193 221357 . + . ID=NBlab01G00070.2.exon2;Parent=NBlab01G00070.2NbV1Ch01 > AUGUSTUS exon 221469 221529 . + . > ID=NBlab01G00070.2.exon3;Parent=NBlab01G00070.2NbV1Ch01 AUGUSTUS exon > 221625 222022 . + . ID=NBlab01G00070.2.exon4;Parent=NBlab01G00070.2NbV1Ch01 > AUGUSTUS CDS 221010 221012 0.73 + 0 > ID=NBlab01G00070.2.CDS1;Parent=NBlab01G00070.2NbV1Ch01 AUGUSTUS CDS 221193 > 221357 0.72 + 0 ID=NBlab01G00070.2.CDS2;Parent=NBlab01G00070.2NbV1Ch01 > AUGUSTUS CDS 221469 221529 1 + 0 > ID=NBlab01G00070.2.CDS3;Parent=NBlab01G00070.2NbV1Ch01 AUGUSTUS CDS 221625 > 221884 0.94 + 2 ID=NBlab01G00070.2.CDS4;Parent=NBlab01G00070.2NbV1Ch01 > AUGUSTUS five_prime_utr 220636 221009 0.23 + . > ID=NBlab01G00070.2.5UTR1;Parent=NBlab01G00070.2NbV1Ch01 AUGUSTUS intron > 221013 221192 0.72 + . > ID=NBlab01G00070.2.intron1;Parent=NBlab01G00070.2NbV1Ch01 AUGUSTUS intron > 221358 221468 0.74 + . > ID=NBlab01G00070.2.intron2;Parent=NBlab01G00070.2NbV1Ch01 AUGUSTUS intron > 221530 221624 1 + . > ID=NBlab01G00070.2.intron3;Parent=NBlab01G00070.2NbV1Ch01 AUGUSTUS > start_codon 221010 221012 . + 0 > ID=NBlab01G00070.2.SCodon1;Parent=NBlab01G00070.2NbV1Ch01 AUGUSTUS > stop_codon 221882 221884 . + 0 > ID=NBlab01G00070.2.ECodon1;Parent=NBlab01G00070.2NbV1Ch01 AUGUSTUS > three_prime_utr 221885 222022 0.44 + . > ID=NBlab01G00070.2.3UTR1;Parent=NBlab01G00070.2NbV1Ch01 AUGUSTUS > transcription_end_site 222022 222022 . + . > ID=NBlab01G00070.2.TES1;Parent=NBlab01G00070.2NbV1Ch01 AUGUSTUS > transcription_start_site 220636 220636 . + . > ID=NBlab01G00070.2.TSS1;Parent=NBlab01G00070.2NbV1Ch01 AUGUSTUS mRNA 221156 > 222022 0.43 + . ID=NBlab01G00070.1;Note=P34 probable thiol > protease;Parent=NBlab01G00070NbV1Ch01 AUGUSTUS exon 221156 221305 . + . > ID=NBlab01G00070.1.exon1;Parent=NBlab01G00070.1NbV1Ch01 AUGUSTUS exon > 221469 221529 . + . ID=NBlab01G00070.1.exon2;Parent=NBlab01G00070.1NbV1Ch01 > AUGUSTUS exon 221625 222022 . + . > ID=NBlab01G00070.1.exon3;Parent=NBlab01G00070.1NbV1Ch01 AUGUSTUS CDS 221231 > 221305 1 + 0 ID=NBlab01G00070.1.CDS1;Parent=NBlab01G00070.1NbV1Ch01 > AUGUSTUS CDS 221469 221529 1 + 0 > ID=NBlab01G00070.1.CDS2;Parent=NBlab01G00070.1NbV1Ch01 AUGUSTUS CDS 221625 > 221884 0.99 + 2 ID=NBlab01G00070.1.CDS3;Parent=NBlab01G00070.1NbV1Ch01 > AUGUSTUS five_prime_utr 221156 221230 0.7 + . > ID=NBlab01G00070.1.5UTR1;Parent=NBlab01G00070.1NbV1Ch01 AUGUSTUS intron > 221306 221468 1 + . > ID=NBlab01G00070.1.intron1;Parent=NBlab01G00070.1NbV1Ch01 AUGUSTUS intron > 221530 221624 1 + . > ID=NBlab01G00070.1.intron2;Parent=NBlab01G00070.1NbV1Ch01 AUGUSTUS > start_codon 221231 221233 . + 0 > ID=NBlab01G00070.1.SCodon1;Parent=NBlab01G00070.1NbV1Ch01 AUGUSTUS > stop_codon 221882 221884 . + 0 > ID=NBlab01G00070.1.ECodon1;Parent=NBlab01G00070.1NbV1Ch01 AUGUSTUS > three_prime_utr 221885 222022 0.59 + . > ID=NBlab01G00070.1.3UTR1;Parent=NBlab01G00070.1NbV1Ch01 AUGUSTUS > transcription_end_site 222022 222022 . + . > ID=NBlab01G00070.1.TES1;Parent=NBlab01G00070.1NbV1Ch01 AUGUSTUS > transcription_start_site 221156 221156 . + . > ID=NBlab01G00070.1.TSS1;Parent=NBlab01G00070.1...* > > What did I miss? > > Thank you in advance, > > Michal > _______________________________________________ > Gmod-ajax mailing list > Gmo...@li... > https://lists.sourceforge.net/lists/listinfo/gmod-ajax > |
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From: Michał T. L. <m.t...@gm...> - 2020-02-02 16:32:17
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Hi all, After the running the below command I got *WARNING: No matching features found for mRNA *and the track is empty: *$ perl ~/tomcat7-deploy/apollo/jbrowse/bin/flatfile-to-json.pl <http://flatfile-to-json.pl> --nameAttributes "ID,Name,Note" --gff /efs/apollo/QUT NbRNASeqAll.sorted-proper.add-rg.bam.dedup.bam.gtf.fasta.transdecoder.genome.FixVSaugustus.hints_utrAGAT.newID-swissprot.filtered.gff3 --compress --trackType HTMLFeatures --trackLabel "NbRNASeqAll.sorted-proper.add-rg.bam.dedup.bam.gtf.fasta.transdecoder.genome.FixVSaugustus.hints_utrAGAT.newID-swissprot.filtered" --type=mRNA --out /efs/apollo/QUTWARNING: No matching features found for mRNA* *$ head -n 100 NbRNASeqAll.sorted-proper.add-rg.bam.dedup.bam.gtf.fasta.transdecoder.genome.FixVSaugustus.hints_utrAGAT.newID-swissprot.filtered.gff3##gff-version 3##sequence-region NbV1Ch01 1 187320599NbV1Ch01 transdecoder gene 98185 99705 . - . ID=NBlab01G00010NbV1Ch01 transdecoder mRNA 98185 99705 . - . ID=NBlab01G00010.1;Note=Peroxidase 40;Parent=NBlab01G00010NbV1Ch01 transdecoder exon 98185 98571 . - . ID=NBlab01G00010.1.exon4;Parent=NBlab01G00010.1NbV1Ch01 transdecoder exon 98679 98844 . - . ID=NBlab01G00010.1.exon3;Parent=NBlab01G00010.1NbV1Ch01 transdecoder exon 99134 99325 . - . ID=NBlab01G00010.1.exon2;Parent=NBlab01G00010.1NbV1Ch01 transdecoder exon 99417 99705 . - . ID=NBlab01G00010.1.exon1;Parent=NBlab01G00010.1NbV1Ch01 transdecoder CDS 98186 98571 . - 2 ID=NBlab01G00010.1.cds;Parent=NBlab01G00010.1NbV1Ch01 transdecoder CDS 98679 98844 . - 0 ID=NBlab01G00010.1.cds;Parent=NBlab01G00010.1NbV1Ch01 transdecoder CDS 99134 99325 . - 0 ID=NBlab01G00010.1.cds;Parent=NBlab01G00010.1NbV1Ch01 transdecoder CDS 99417 99704 . - 0 ID=NBlab01G00010.1.cds;Parent=NBlab01G00010.1NbV1Ch01 transdecoder five_prime_UTR 99705 99705 . - . ID=NBlab01G00010.1.5UTRg1;Parent=NBlab01G00010.1NbV1Ch01 transdecoder three_prime_UTR 98185 98185 . - . ID=NBlab01G00010.1.3UTRg1;Parent=NBlab01G00010.1NbV1Ch01 transdecoder gene 212254 223251 . - . ID=NBlab01G00060NbV1Ch01 transdecoder mRNA 212254 223251 . - . ID=NBlab01G00060.1;Note=P34 probable thiol protease;Parent=NBlab01G00060NbV1Ch01 transdecoder exon 212254 212731 . - . ID=NBlab01G00060.1.exon5;Parent=NBlab01G00060.1NbV1Ch01 transdecoder exon 212829 212968 . - . ID=NBlab01G00060.1.exon4;Parent=NBlab01G00060.1NbV1Ch01 transdecoder exon 218080 219546 . - . ID=NBlab01G00060.1.exon3;Parent=NBlab01G00060.1NbV1Ch01 transdecoder exon 219642 222881 . - . ID=NBlab01G00060.1.exon2;Parent=NBlab01G00060.1NbV1Ch01 transdecoder exon 222989 223251 . - . ID=NBlab01G00060.1.exon1;Parent=NBlab01G00060.1NbV1Ch01 transdecoder CDS 219287 219546 . - 2 ID=NBlab01G00060.1.cds;Parent=NBlab01G00060.1NbV1Ch01 transdecoder CDS 219642 219711 . - 0 ID=NBlab01G00060.1.cds;Parent=NBlab01G00060.1NbV1Ch01 transdecoder five_prime_UTR 219712 222881 . - . ID=NBlab01G00060.1.utr5p2;Parent=NBlab01G00060.1NbV1Ch01 transdecoder five_prime_UTR 222989 223251 . - . ID=NBlab01G00060.1.utr5p1;Parent=NBlab01G00060.1NbV1Ch01 transdecoder three_prime_UTR 212254 212731 . - . ID=NBlab01G00060.1.utr3p3;Parent=NBlab01G00060.1NbV1Ch01 transdecoder three_prime_UTR 212829 212968 . - . ID=NBlab01G00060.1.utr3p2;Parent=NBlab01G00060.1NbV1Ch01 transdecoder three_prime_UTR 218080 219286 . - . ID=NBlab01G00060.1.utr3p1;Parent=NBlab01G00060.1NbV1Ch01 transdecoder mRNA 212254 223251 . - . ID=NBlab01G00060.2;Note=Cysteine proteinase COT44 %28Fragment%29;Parent=NBlab01G00060NbV1Ch01 transdecoder exon 212254 212731 . - . ID=NBlab01G00060.2.exon8;Parent=NBlab01G00060.2NbV1Ch01 transdecoder exon 212829 212968 . - . ID=NBlab01G00060.2.exon7;Parent=NBlab01G00060.2NbV1Ch01 transdecoder exon 218080 218969 . - . ID=NBlab01G00060.2.exon6;Parent=NBlab01G00060.2NbV1Ch01 transdecoder exon 219061 219198 . - . ID=NBlab01G00060.2.exon5;Parent=NBlab01G00060.2NbV1Ch01 transdecoder exon 219271 219546 . - . ID=NBlab01G00060.2.exon4;Parent=NBlab01G00060.2NbV1Ch01 transdecoder exon 219642 219702 . - . ID=NBlab01G00060.2.exon3;Parent=NBlab01G00060.2NbV1Ch01 transdecoder exon 219814 222881 . - . ID=NBlab01G00060.2.exon2;Parent=NBlab01G00060.2NbV1Ch01 transdecoder exon 222989 223251 . - . ID=NBlab01G00060.2.exon1;Parent=NBlab01G00060.2NbV1Ch01 transdecoder CDS 218733 218969 . - 0 ID=NBlab01G00060.2.cds;Parent=NBlab01G00060.2NbV1Ch01 transdecoder CDS 219061 219198 . - 0 ID=NBlab01G00060.2.cds;Parent=NBlab01G00060.2NbV1Ch01 transdecoder CDS 219271 219345 . - 0 ID=NBlab01G00060.2.cds;Parent=NBlab01G00060.2NbV1Ch01 transdecoder five_prime_UTR 219346 219546 . - . ID=NBlab01G00060.2.utr5p4;Parent=NBlab01G00060.2NbV1Ch01 transdecoder five_prime_UTR 219642 219702 . - . ID=NBlab01G00060.2.utr5p3;Parent=NBlab01G00060.2NbV1Ch01 transdecoder five_prime_UTR 219814 222881 . - . ID=NBlab01G00060.2.utr5p2;Parent=NBlab01G00060.2NbV1Ch01 transdecoder five_prime_UTR 222989 223251 . - . ID=NBlab01G00060.2.utr5p1;Parent=NBlab01G00060.2NbV1Ch01 transdecoder three_prime_UTR 212254 212731 . - . ID=NBlab01G00060.2.utr3p3;Parent=NBlab01G00060.2NbV1Ch01 transdecoder three_prime_UTR 212829 212968 . - . ID=NBlab01G00060.2.utr3p2;Parent=NBlab01G00060.2NbV1Ch01 transdecoder three_prime_UTR 218080 218732 . - . ID=NBlab01G00060.2.utr3p1;Parent=NBlab01G00060.2NbV1Ch01 transdecoder mRNA 212254 223251 . - . ID=NBlab01G00060.3;Note=P34 probable thiol protease;Parent=NBlab01G00060NbV1Ch01 transdecoder exon 212254 212731 . - . ID=NBlab01G00060.3.exon7;Parent=NBlab01G00060.3NbV1Ch01 transdecoder exon 212829 212968 . - . ID=NBlab01G00060.3.exon6;Parent=NBlab01G00060.3NbV1Ch01 transdecoder exon 218080 218386 . - . ID=NBlab01G00060.3.exon5;Parent=NBlab01G00060.3NbV1Ch01 transdecoder exon 219061 219546 . - . ID=NBlab01G00060.3.exon4;Parent=NBlab01G00060.3NbV1Ch01 transdecoder exon 219642 219702 . - . ID=NBlab01G00060.3.exon3;Parent=NBlab01G00060.3NbV1Ch01 transdecoder exon 219866 222881 . - . ID=NBlab01G00060.3.exon2;Parent=NBlab01G00060.3NbV1Ch01 transdecoder exon 222989 223251 . - . ID=NBlab01G00060.3.exon1;Parent=NBlab01G00060.3NbV1Ch01 transdecoder CDS 219287 219546 . - 2 ID=NBlab01G00060.3.cds;Parent=NBlab01G00060.3NbV1Ch01 transdecoder CDS 219642 219702 . - 0 ID=NBlab01G00060.3.cds;Parent=NBlab01G00060.3NbV1Ch01 transdecoder CDS 219866 219940 . - 0 ID=NBlab01G00060.3.cds;Parent=NBlab01G00060.3NbV1Ch01 transdecoder five_prime_UTR 219941 222881 . - . ID=NBlab01G00060.3.utr5p2;Parent=NBlab01G00060.3NbV1Ch01 transdecoder five_prime_UTR 222989 223251 . - . ID=NBlab01G00060.3.utr5p1;Parent=NBlab01G00060.3NbV1Ch01 transdecoder three_prime_UTR 212254 212731 . - . ID=NBlab01G00060.3.utr3p4;Parent=NBlab01G00060.3NbV1Ch01 transdecoder three_prime_UTR 212829 212968 . - . ID=NBlab01G00060.3.utr3p3;Parent=NBlab01G00060.3NbV1Ch01 transdecoder three_prime_UTR 218080 218386 . - . ID=NBlab01G00060.3.utr3p2;Parent=NBlab01G00060.3NbV1Ch01 transdecoder three_prime_UTR 219061 219286 . - . ID=NBlab01G00060.3.utr3p1;Parent=NBlab01G00060.3NbV1Ch01 AUGUSTUS gene 220636 222022 0.53 + . ID=NBlab01G00070NbV1Ch01 AUGUSTUS mRNA 220636 222022 0.1 + . ID=NBlab01G00070.2;Note=P34 probable thiol protease;Parent=NBlab01G00070NbV1Ch01 AUGUSTUS exon 220636 221012 . + . ID=NBlab01G00070.2.exon1;Parent=NBlab01G00070.2NbV1Ch01 AUGUSTUS exon 221193 221357 . + . ID=NBlab01G00070.2.exon2;Parent=NBlab01G00070.2NbV1Ch01 AUGUSTUS exon 221469 221529 . + . ID=NBlab01G00070.2.exon3;Parent=NBlab01G00070.2NbV1Ch01 AUGUSTUS exon 221625 222022 . + . ID=NBlab01G00070.2.exon4;Parent=NBlab01G00070.2NbV1Ch01 AUGUSTUS CDS 221010 221012 0.73 + 0 ID=NBlab01G00070.2.CDS1;Parent=NBlab01G00070.2NbV1Ch01 AUGUSTUS CDS 221193 221357 0.72 + 0 ID=NBlab01G00070.2.CDS2;Parent=NBlab01G00070.2NbV1Ch01 AUGUSTUS CDS 221469 221529 1 + 0 ID=NBlab01G00070.2.CDS3;Parent=NBlab01G00070.2NbV1Ch01 AUGUSTUS CDS 221625 221884 0.94 + 2 ID=NBlab01G00070.2.CDS4;Parent=NBlab01G00070.2NbV1Ch01 AUGUSTUS five_prime_utr 220636 221009 0.23 + . ID=NBlab01G00070.2.5UTR1;Parent=NBlab01G00070.2NbV1Ch01 AUGUSTUS intron 221013 221192 0.72 + . ID=NBlab01G00070.2.intron1;Parent=NBlab01G00070.2NbV1Ch01 AUGUSTUS intron 221358 221468 0.74 + . ID=NBlab01G00070.2.intron2;Parent=NBlab01G00070.2NbV1Ch01 AUGUSTUS intron 221530 221624 1 + . ID=NBlab01G00070.2.intron3;Parent=NBlab01G00070.2NbV1Ch01 AUGUSTUS start_codon 221010 221012 . + 0 ID=NBlab01G00070.2.SCodon1;Parent=NBlab01G00070.2NbV1Ch01 AUGUSTUS stop_codon 221882 221884 . + 0 ID=NBlab01G00070.2.ECodon1;Parent=NBlab01G00070.2NbV1Ch01 AUGUSTUS three_prime_utr 221885 222022 0.44 + . ID=NBlab01G00070.2.3UTR1;Parent=NBlab01G00070.2NbV1Ch01 AUGUSTUS transcription_end_site 222022 222022 . + . ID=NBlab01G00070.2.TES1;Parent=NBlab01G00070.2NbV1Ch01 AUGUSTUS transcription_start_site 220636 220636 . + . ID=NBlab01G00070.2.TSS1;Parent=NBlab01G00070.2NbV1Ch01 AUGUSTUS mRNA 221156 222022 0.43 + . ID=NBlab01G00070.1;Note=P34 probable thiol protease;Parent=NBlab01G00070NbV1Ch01 AUGUSTUS exon 221156 221305 . + . ID=NBlab01G00070.1.exon1;Parent=NBlab01G00070.1NbV1Ch01 AUGUSTUS exon 221469 221529 . + . ID=NBlab01G00070.1.exon2;Parent=NBlab01G00070.1NbV1Ch01 AUGUSTUS exon 221625 222022 . + . ID=NBlab01G00070.1.exon3;Parent=NBlab01G00070.1NbV1Ch01 AUGUSTUS CDS 221231 221305 1 + 0 ID=NBlab01G00070.1.CDS1;Parent=NBlab01G00070.1NbV1Ch01 AUGUSTUS CDS 221469 221529 1 + 0 ID=NBlab01G00070.1.CDS2;Parent=NBlab01G00070.1NbV1Ch01 AUGUSTUS CDS 221625 221884 0.99 + 2 ID=NBlab01G00070.1.CDS3;Parent=NBlab01G00070.1NbV1Ch01 AUGUSTUS five_prime_utr 221156 221230 0.7 + . ID=NBlab01G00070.1.5UTR1;Parent=NBlab01G00070.1NbV1Ch01 AUGUSTUS intron 221306 221468 1 + . ID=NBlab01G00070.1.intron1;Parent=NBlab01G00070.1NbV1Ch01 AUGUSTUS intron 221530 221624 1 + . ID=NBlab01G00070.1.intron2;Parent=NBlab01G00070.1NbV1Ch01 AUGUSTUS start_codon 221231 221233 . + 0 ID=NBlab01G00070.1.SCodon1;Parent=NBlab01G00070.1NbV1Ch01 AUGUSTUS stop_codon 221882 221884 . + 0 ID=NBlab01G00070.1.ECodon1;Parent=NBlab01G00070.1NbV1Ch01 AUGUSTUS three_prime_utr 221885 222022 0.59 + . ID=NBlab01G00070.1.3UTR1;Parent=NBlab01G00070.1NbV1Ch01 AUGUSTUS transcription_end_site 222022 222022 . + . ID=NBlab01G00070.1.TES1;Parent=NBlab01G00070.1NbV1Ch01 AUGUSTUS transcription_start_site 221156 221156 . + . ID=NBlab01G00070.1.TSS1;Parent=NBlab01G00070.1...* What did I miss? Thank you in advance, Michal |
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From: Robin H. <Rob...@oi...> - 2020-01-28 21:34:14
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Dear All, Sorry for the multiple postings! The Open Genome Informatics team serves as an “umbrella" organization to support the efforts of many open access open-source bioinformatics projects for Google Summer of Code (GSoC)<https://summerofcode.withgoogle.com/>. Among this list of projects are GMOD and its software projects -- GBrowse, JBrowse; Galaxy; Reactome; WormBase; DockStore; Bioconda; and others. Call for 2020 Project Ideas and Mentors: We are seeking project ideas to post and attract talented students to this year’s Summer of Code competition. If you have a project idea for which you would like to mentor a student, please contact Robin Haw, Marc Gillespie, Dave Clements, Dannon Baker, and Scott Cain (emails above). You can also submit your ideas here<http://gmod.org/wiki/GSOC_Project_Ideas_2020>. For more information please refer to the Open Genome Informatics page on the GMOD.org website<http://gmod.org/wiki/GSoC#Google_Summer_of_Code_2020>. The mentoring organization application deadline with GSoC is February 5th at 2 pm EST. So, if you are interested in taking part with the team please let us know as soon as possible. Please forward this to others who might be interested in taking part. If you have any questions please let us know. Thanks, Robin, Marc, Dave, Dannon, and Scott. Robin Haw, PhD Reactome | JBrowse - Senior Project Manager and Outreach Co-ordinator rob...@oi...<mailto:rob...@oi...> Ontario Institute for Cancer Research MaRS Centre, 661 University Avenue, Suite 510, Toronto, Ontario, Canada M5G 0A3 @OICR_news | www.oicr.on.ca | @reactome | reactome.org | @JBrowseGossip | jbrowse.org Collaborate. Translate. Change lives. This message and any attachments may contain confidential and/or privileged information for the sole use of the intended recipient. Any review or distribution by anyone other than the person for whom it was originally intended is strictly prohibited. If you have received this message in error, please contact the sender and delete all copies. Opinions, conclusions or other information contained in this message may not be that of the organization. |
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