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

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

Hi Julia,

At first, I thought the colon ":" in the reference sequence name was going
to cause a problem, but it appears to work (Colin told me it worked for
him).  Usually when you open the javascript console, you'll get the error
console by default, so I would guess that's what you saw. If you want to
send a screenshot to make sure, that would be fine.

Finally, if you want to/can, you are welcome to send the sequence and bam
files to me individually and I can try to see if I can sort out what's
going on.

Scott



On Tue, Jun 2, 2020 at 1:24 AM Zieringer, Julia <
jul...@ib...> wrote:

> Hi Scott,
>
>
>
> there is nothing showing up when i open the bam and bai file. I checked
> the name oft he reference sequence and it is the same in the bam file, as
> far as i can tell…
>
> Reference file:
>
> Corresponding Bam file:
>
>
>
>
>
> I used the debug tool in the desktop app (unfortunately Jbrowse is not
> available on our galaxy server yet) to see if an error message is showing
> up in the console, but nothing happened here. However i am not sure if i
> look at the right part of the debuger? I am not familiar with this tool.
>
>
>
> Thanks a lot for your help,
>
> Julia
>
>
>
>
>
>
>
>
>
> *Von:* Scott Cain [mailto:sc...@sc...]
> *Gesendet:* Freitag, 29. Mai 2020 20:27
> *An:* Zieringer, Julia <jul...@ib...>
> *Cc:* gmo...@li...
> *Betreff:* Re: [Gmod-ajax] can not load bam file
>
>
>
> 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
>
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> 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
>


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