Re: [Gmod-ajax] JBrowse bigwig tracks showing no plot/data when there should be

[Scott C. <sc...@sc...>]

Hi Vaneet,

What are the chances that the names of the reference sequence in the files
are like 1,2,3 and in JBrowse they are chr1, chr2, chr3...(or some similar
name conflict, like the genbank accession number)? JBrowse 1 isn't
brilliant at dealing with these issues (I recall having to hack JB to deal
with the fact that sometimes people refer to worm genes like chrI, chrV
instead of I, V, etc)

If that's not it, I'm not sure what it might be--are there any messages in
the js console?

Scott


On Fri, Jun 23, 2023 at 2:48 PM Vaneet Lotay <van...@uc...>
wrote:

> Hello,
>
>
>
> I’ve had this issue several times with different batches of RNA-Seq data,
> related to Echinoderms.  I load a batch of bigwig data tracks and see no
> visible amplitude or plot anywhere I search in the corresponding genome for
> any of the tracks.  I attached a screenshot with a few of the tracks and
> the info box I opened which shows that there should be some score to plot
> from what I understand, looking at the mean and max values.  Yet I still
> see nothing plotted.  The person I was working with added the tracks to the
> IGV browser and it showed that there is data there (screenshot attached),
> that’s why I’m wondering what’s going on?  Is there some configuration
> setting I need to enable to show the data which I haven’t thought of?  I
> can separately send you a link to my JBrowse or send you some of the tracks
> perhaps for further debugging.
>
>
>
> Thanks,
>
>
> Vaneet
>
>
>
> *Vaneet Lotay*
>
> *Xenbase Bioinformatician*
>
> *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
>


-- 
------------------------------------------------------------------------
Scott Cain, Ph. D.                                                  scott
at scottcain dot net
GMOD Project Manager (http://gmod.org/)
216-392-3087
WormBase Developer (http://wormbase.org/)
Alliance of Genome Resources Group Leader (http://alliancegenome.org/)
VirusSeq Project Manager (https://virusseq-dataportal.ca/)
Human Cancer Models Initiative Project Manager (
https://hcmi-searchable-catalog.nci.nih.gov/)