Re: [Gmod-ajax] can not load bam file

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

Hi Julia,

Did the track show up but it was empty? If so, my first guess would be that
the name of the reference sequence in the BAM file doesn't agree with the
name of the reference sequence in the rest of JBrowse.  If that's not
what's going on, can you open up the browser's javascript console (under
View in chrome, under Developer in Safari and under Tools in Firefox) and
see if there are any error messages that might point to what the problem is?

If it's available on a public server, if you could give us the url (via
private email if necessary) we can take a look to see if we can figure it
out.

Scott


On Fri, May 29, 2020 at 11:09 AM Zieringer, Julia <
jul...@ib...> wrote:

> Hello,
>
>
>
> my name is Julia and I am from Germany. I used snippy on a Galaxy server
> to identify variants between two genomes. Ti visualize the variants and
> coverage I want to import the fasta sequence file of my reference, the
> variants from the gff3 and the bam file to see the alignments in the
> desktop app of JBrowse. I can import the sequence fasta file of my
> reference and the corresponding gff3 file with the variants without a
> problem, however as soon as i want to load the bam (and Bam index file bai)
> it is not working.
>
>
>
> I go to track (ater i loaded the genome sequence) and load both, the bam
> and bai file. Afterwards i simply click open and the import-window
> disapears but nothing is showing up?! I do not know what is going on… or if
> something is missing?
>
>
>
> Thank you very much,
>
> Julia
> _______________________________________________
> Gmod-ajax mailing list
> Gmo...@li...
> https://lists.sourceforge.net/lists/listinfo/gmod-ajax
>


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