Re: [Gmod-ajax] Combining BigWig Tracks

[Colin <col...@gm...>]

Good catch

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

https://github.com/GMOD/jbrowse/pull/1536

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
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...> 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...>
> *Sent:* Wednesday, August 5, 2020 8:28 PM
> *To:* ARORA, SONNY <sz...@ps...>
> *Cc:* gmo...@li... <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%7Ce01d5630504d430a136208d8399fb416%7C7cf48d453ddb4389a9c1c115526eb52e%7C0%7C0%7C637322705374494356&sdata=SfwFQ0uT5uEfnRHKxZUCy20YzRIS4K%2BsIprPJaM1jLg%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%7Ce01d5630504d430a136208d8399fb416%7C7cf48d453ddb4389a9c1c115526eb52e%7C0%7C0%7C637322705374504350&sdata=c7ZlfwvpGLRSurpON%2FbexVulpsAugoC2QUG7cOv%2BCqk%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...> 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%7Ce01d5630504d430a136208d8399fb416%7C7cf48d453ddb4389a9c1c115526eb52e%7C0%7C0%7C637322705374504350&sdata=gNua150N%2BaRtEDXCOhCEIz9%2BLIvC1g6XpPWUhKMxjQk%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
>
>
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