Re: [Gmod-ajax] Combining BigWig Tracks

[ARORA, S. <sz...@ps...>]

Great, thanks for taking care of that so quickly!
________________________________
From: Colin <col...@gm...>
Sent: Friday, August 7, 2020 3:23 PM
To: ARORA, SONNY <sz...@ps...>
Cc: gmo...@li... <gmo...@li...>
Subject: Re: [Gmod-ajax] Combining BigWig Tracks

Good catch

The fix is similar to the above answer, but needed fixing in our core codebase

https://github.com/GMOD/jbrowse/pull/1536<https://nam01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2FGMOD%2Fjbrowse%2Fpull%2F1536&data=02%7C01%7Csza149%40psu.edu%7C9a381f6d188a4ab31ec408d83b0774dc%7C7cf48d453ddb4389a9c1c115526eb52e%7C0%7C0%7C637324250497994478&sdata=txhdawuYNFp2NGX6s%2Fk9ajO6Yvzc2tstEUr76XImpUk%3D&reserved=0>

This is an example of where we have had combination tracks for a long time but we never got this bug noticed, I think they are also very cool but indeed not often used.

If you are interested you can check out this branch and create a custom build

git clone https://github.com/gmod/jbrowse<https://nam01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2Fgmod%2Fjbrowse&data=02%7C01%7Csza149%40psu.edu%7C9a381f6d188a4ab31ec408d83b0774dc%7C7cf48d453ddb4389a9c1c115526eb52e%7C0%7C0%7C637324250498004479&sdata=UvL7lbsGFocN63YO4bpJtjl1XjrWr3W8MeekOikvIgI%3D&reserved=0>
cd jbrowse
git checkout fix_local_combination
./setup.sh

Should be able to get merged and released sometime soon though

-Colin

On Fri, Aug 7, 2020 at 2:07 PM ARORA, SONNY <sz...@ps...<mailto:sz...@ps...>> wrote:
Thanks! That worked great when adding tracks with the API.

Any idea what was going wrong when I was adding bigwigs through the navbar and trying to use a combination track? Sometimes users would like to add local tracks to JBrowse and I was hoping to allow them to do that through the navbar with the ability to use them in a combination track.

> Note that we don't use combination tracks often so there are probably some weird corners there, but I am curious how your experience goes

That's a shame that they are not used so often. A big reason my lab is interested in JBrowse is because we were looking for a well supported web-based browser with the combination track feature. Often members of our lab want to visually combine replicates for experiments and it's a bit of a pain to create a merged big wig for those cases. Are you aware of any areas where I might run into issues with combination tracks? Thanks again for all your help so far!
________________________________
From: Colin <col...@gm...<mailto:col...@gm...>>
Sent: Wednesday, August 5, 2020 8:28 PM
To: ARORA, SONNY <sz...@ps...<mailto:sz...@ps...>>
Cc: gmo...@li...<mailto:gmo...@li...> <gmo...@li...<mailto:gmo...@li...>>
Subject: Re: [Gmod-ajax] Combining BigWig Tracks

I think this is sort of related to your last question (xref https://sourceforge.net/p/gmod/mailman/message/37078566/<https://nam01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fsourceforge.net%2Fp%2Fgmod%2Fmailman%2Fmessage%2F37078566%2F&data=02%7C01%7Csza149%40psu.edu%7C9a381f6d188a4ab31ec408d83b0774dc%7C7cf48d453ddb4389a9c1c115526eb52e%7C0%7C0%7C637324250498004479&sdata=ljVFg6%2BAP70c%2Fw07VeWg6OwJW97M6zptgyoQRU5U4CY%3D&reserved=0>)

I took a little shortcut and made an abbreviated config in that thread, but if you add the storeClass to the track config, then the Combination track recognizes it properly and should allow it


var storeName = JBrowse.addStoreConfig(null, {
  browser: JBrowse,
  type: "JBrowse/Store/SeqFeature/BigWig",
  baseUrl: ".",
  urlTemplate: "sample_data/raw/volvox/volvox_microarray.bw<https://nam01.safelinks.protection.outlook.com/?url=http%3A%2F%2Fvolvox_microarray.bw%2F&data=02%7C01%7Csza149%40psu.edu%7C9a381f6d188a4ab31ec408d83b0774dc%7C7cf48d453ddb4389a9c1c115526eb52e%7C0%7C0%7C637324250498014469&sdata=2bEgTZsjtuf%2BO4%2BZSHNQI1PVW0xp4ZNp0DzV%2FlgMSIk%3D&reserved=0>",
});
JBrowse.publish("/jbrowse/v1/v/tracks/replace", [
  { label: "My Track2", store: storeName, storeClass: "JBrowse/Store/SeqFeature/BigWig" },
]);

Note that we don't use combination tracks often so there are probably some weird corners there, but I am curious how your experience goes

-Colin

On Wed, Aug 5, 2020 at 5:42 PM ARORA, SONNY <sz...@ps...<mailto:sz...@ps...>> wrote:
Hi,

I'm looking to add two bigwigs together in JBrowse. I'm working on Chrome Version 84.0.4147.89 (Official Build) (64-bit).

Going to the address:

http://jbrowse.org/code/JBrowse-1.16.9/?data=sample_data%2Fjson%2Fvolvox&loc=ctgA%3A19987..24704&tracks=DNA%2Cvolvox_microarray_bw_density%2Cvolvox_sine_density&highlight=<https://nam01.safelinks.protection.outlook.com/?url=http%3A%2F%2Fjbrowse.org%2Fcode%2FJBrowse-1.16.9%2F%3Fdata%3Dsample_data%252Fjson%252Fvolvox%26loc%3DctgA%253A19987..24704%26tracks%3DDNA%252Cvolvox_microarray_bw_density%252Cvolvox_sine_density%26highlight%3D&data=02%7C01%7Csza149%40psu.edu%7C9a381f6d188a4ab31ec408d83b0774dc%7C7cf48d453ddb4389a9c1c115526eb52e%7C0%7C0%7C637324250498014469&sdata=kTmKJnyt28wmhydGOTJNBBp6V5P4QmFnn1zyj%2Ftlmyo%3D&reserved=0>

I add a genome by clicking Genome -> Open Sequence File -> Local Files -> Select Files. I then select my mm10.fa and mm10.fa.fai files and click open.

I then load two bigwigs: Track -> Open track file or URL -> Local Files -> Select Files. The bigwigs appear to display fine.

I create a combination track: Track -> Add combination track.

When I try to drag over one of the bigwigs to the combination track I get a red stop sign and am not able to add the bigwig to the track. I've attached a screenshot. Let me know what I'm doing wrong, thanks!

Best,

Sonny


_______________________________________________
Gmod-ajax mailing list
Gmo...@li...<mailto:Gmo...@li...>
https://lists.sourceforge.net/lists/listinfo/gmod-ajax<https://nam01.safelinks.protection.outlook.com/?url=https%3A%2F%2Flists.sourceforge.net%2Flists%2Flistinfo%2Fgmod-ajax&data=02%7C01%7Csza149%40psu.edu%7C9a381f6d188a4ab31ec408d83b0774dc%7C7cf48d453ddb4389a9c1c115526eb52e%7C0%7C0%7C637324250498024469&sdata=2EvBOmwf3dtBcGPrZAOVbiOOh%2Ft%2BuWT3kOxLnkPLcMc%3D&reserved=0>