Dear Shashi, For any questions you might have about SAMtools, please contact: [email protected]. Hope this helps.
Vanessa Kirkup Swing UCSC Genome Bioinformatics Group ----- Original Message ----- From: "Shashikant Pujar" <[email protected]> To: "Maximilian Haussler" <[email protected]> Cc: [email protected] Sent: Thursday, June 3, 2010 5:34:57 AM GMT -08:00 US/Canada Pacific Subject: Re: [Genome] Custom Track Question Jennifer and Max Thanks for your replies. I think it is something to do with Galaxy too. I will contact them about the filter pileup not loading on the Browser. Jennifer, one quick novice question. I did go through SAMTools documentation, and it appears that it is built for UNIX environment. However, I did see a .....win32 file. So can SAMTools be run in Windows-MSDos? Shashi ________________________________________ From: Maximilian Haussler [[email protected]] Sent: Wednesday, June 02, 2010 6:16 PM To: Shashikant Pujar Cc: Jennifer Jackson; [email protected] Subject: Re: [Genome] Custom Track Question 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]<mailto:[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]<mailto:[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]<mailto:[email protected]>] Sent: Wednesday, June 02, 2010 2:46 PM To: Shashikant Pujar Cc: [email protected]<mailto:[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]<mailto:[email protected]> > https://lists.soe.ucsc.edu/mailman/listinfo/genome _______________________________________________ Genome maillist - [email protected]<mailto:[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
