Galaxy is a separate website, not directly related to the UCSC genome
browser.
>From what I understand ("it is not loading"), your problem could be due to
Galaxy.
You can tell them what you did (including a link to your galaxy session) and
why you think the pileup in Galaxy is not working, just contact them
directly: [email protected], they can probably better help you with
this question.
good luck
Max
On Wed, Jun 2, 2010 at 8:17 PM, Shashikant Pujar <[email protected]> wrote:
> Hello Jennifer
> Thanks for your reply. I am not familiar with SAMTools in UCSC Browser, so
> it is difficult for me to do the command line thing.
> I tried to load the "Filter pileup" on to the UCSC Genome Browser within
> Galaxy, but it is not loading. I also tried the tabular version of the
> "Filter pileup", with the same outcome. Further, I tried to save the Filter
> pileup as a file and load it on the browser (outside Galaxy) but no luck.
> Any suggestions?
> Shashi
>
> ________________________________________
> From: Jennifer Jackson [[email protected]]
> Sent: Wednesday, June 02, 2010 2:46 PM
> To: Shashikant Pujar
> Cc: [email protected]
> Subject: Re: [Genome] Custom Track Question
>
> Hello Shashi,
>
> You have some choices:
>
> Using SAM Tools on the command line, samtools pileup -c will call
> variants from the SAM/BAM alignments with BED output. This could be
> loaded at a custom track. This may be the quickest method if your
> dataset is very large.
>
> Or, you can use Galaxy and load the results as a custom track. Send your
> existing BAM custom track data from the Table browser (if not too large)
> or upload files directly, then after the analysis, view results in the
> UCSC browser. At Galaxy, see "NGS: SAM Tools -> Generate pileup & Filter
> pileup".
>
> Links from UCSC:
> http://genome.ucsc.edu/ -> Galaxy (left blue bar)
> from Table browser: Check "Galaxy" box in output section
> Or directly: http://galaxy.psu.edu/
>
> Hopefully this helps,
> Jennifer
>
> ---------------------------------
> Jennifer Jackson
> UCSC Genome Informatics Group
> http://genome.ucsc.edu/
>
> On 6/2/10 7:03 AM, Shashikant Pujar wrote:
> > Hi
> >
> > I have loaded a custom track (Illumina NGS reads in BAM format of a 2Mb
> region) on the UCSC Dog Genome Browser. Is there a way I can extract all
> SNPs and Indels between the custom track and canFam2?
> >
> > Thanks
> >
> > Shashi Pujar
> > _______________________________________________
> > Genome maillist - [email protected]
> > https://lists.soe.ucsc.edu/mailman/listinfo/genome
>
> _______________________________________________
> Genome maillist - [email protected]
> https://lists.soe.ucsc.edu/mailman/listinfo/genome
>
_______________________________________________
Genome maillist - [email protected]
https://lists.soe.ucsc.edu/mailman/listinfo/genome
