[Gmod-gbrowse] navigating many tracks

[Matthias Monfort]

Dear GBrowse mailing list,
I am a user of GBrowse (mainly through online instances like FlyBase), and I first would like to thank you for the time and effort you put in developing and maintaining GBrowse. I contact the mailing list because I have a question about its features. I would like to know what features exist to address a recurrent use case in my lab, which is the navigation of a lot of track.
For example, in a somewhat common example of current experimental setups, we would have 10 different biological targets (e.g. transcription factors) at 5 different times in 2 different tissues which makes it 50 to 100 signal (reads pileup) tracks, after merging biological and technical replicates. The number doubles (or more) if you add some further analysis tracks (e.g. peak calling tracks, generated with different parameters like the minimum FDR threshold). And of course to complete the information stack you want to visualise those alongside consensus datasets from other projects and studies. This more and more frequent setup raises different issues concerning efficient track navigation and a fruitful visualisation analysis. What features does GBrowse has to address this and ease the navigation of such stacks ?
To be more precise, I have seen that it is possible to create subtracks (my lab has a flybase track divided into subtracks in their browser), which is good. I also read somewhere that one could prevent empty track to show when there is no data (http://gmod.org/wiki/Creating_and_Managing_Subtracks_with_GBrowse2 (http://gmod.org/wiki/Creating_and_Managing_Subtracks_with_GBrowse2)), but can I do that in an instance where I cannot access the server configuration ? Is it specific to certain types of data ? Is there other feature I miss that would allow better navigation of this type of datasets?
Thank you for your help and best regards,
Matthias.

[Scott Cain]

Hi Matthias,

Unfortunately, if you don't have access to the server side configuration,
this is not much you can do in terms of creating subtracks or not showing
empty tracks.

I know you didn't ask about this, but one thing that occurs to me with
regard to your data is faceted browsing, where you can add metadata that
you can sort and filter by, to make it easier for users to find the tracks
they want to see. While GBrowse never got faceted browsing, JBrowse does a
nice job of it. You can see an example here:

http://jbrowse.org/code/JBrowse-1.12.1/index.html?data=sample_data%2Fjson%2Fmodencode&

There are over 1800 tracks in this list but searching it is quite fast and
easy. The tracks and metadata are from fly modENCODE, but the data are all
completely fake; it's just for demoing the track browser.

The one downside with moving to JBrowse (besides an admittadly small
learning curve :-) is that it lacks subtracks. In my opinion, having
faceted track browsing mostly makes up for that, but there are instances
where I'd like to use it.

Scott

Post by Matthias Monfort
Dear GBrowse mailing list,
I am a user of GBrowse (mainly through online instances like FlyBase), and
I first would like to thank you for the time and effort you put in
developing and maintaining GBrowse. I contact the mailing list because I
have a question about its features. I would like to know what features
exist to address a recurrent use case in my lab, which is the navigation of
a lot of track.
For example, in a somewhat common example of current experimental setups,
we would have 10 different biological targets (e.g. transcription factors)
at 5 different times in 2 different tissues which makes it 50 to 100 signal
(reads pileup) tracks, after merging biological and technical replicates.
The number doubles (or more) if you add some further analysis tracks (e.g.
peak calling tracks, generated with different parameters like the minimum
FDR threshold). And of course to complete the information stack you want to
visualise those alongside consensus datasets from other projects and
studies. This more and more frequent setup raises different issues
concerning efficient track navigation and a fruitful visualisation
analysis. What features does GBrowse has to address this and ease the
navigation of such stacks ?
To be more precise, I have seen that it is possible to create subtracks
(my lab has a flybase track divided into subtracks in their browser), which
is good. I also read somewhere that one could prevent empty track to show
when there is no data (http://gmod.org/wiki/Creating_and_Managing_
Subtracks_with_GBrowse2), but can I do that in an instance where I cannot
access the server configuration ? Is it specific to certain types of data ?
Is there other feature I miss that would allow better navigation of this
type of datasets?
Thank you for your help and best regards,
Matthias.
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