navigating many tracks

classic Classic list List threaded Threaded
2 messages Options
Reply | Threaded
Open this post in threaded view
|

navigating many tracks

matthiasm
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.

------------------------------------------------------------------------------
Developer Access Program for Intel Xeon Phi Processors
Access to Intel Xeon Phi processor-based developer platforms.
With one year of Intel Parallel Studio XE.
Training and support from Colfax.
Order your platform today. http://sdm.link/xeonphi
_______________________________________________
Gmod-gbrowse mailing list
[hidden email]
https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse
Reply | Threaded
Open this post in threaded view
|

Re: navigating many tracks

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:


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


On Sat, Nov 12, 2016 at 6:16 AM, Matthias Monfort <[hidden email]> wrote:
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.

------------------------------------------------------------------------------
Developer Access Program for Intel Xeon Phi Processors
Access to Intel Xeon Phi processor-based developer platforms.
With one year of Intel Parallel Studio XE.
Training and support from Colfax.
Order your platform today. http://sdm.link/xeonphi
_______________________________________________
Gmod-gbrowse mailing list
[hidden email]
https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse




--
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     216-392-3087
Ontario Institute for Cancer Research

------------------------------------------------------------------------------

_______________________________________________
Gmod-gbrowse mailing list
[hidden email]
https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse