Quick update: If you are interested in exploring what SAMtools has to offer, here is link to their web site: samtools.sourceforge.net
On 6/2/10 2:39 PM, Jennifer Jackson wrote: > Hi Shashi, > > SAMtools is a distinct software project, presented as a bundle of tools > used to analyze Next-gen sequences and generate/analyze SAM/BAM format > data. It sounds like you did not use this and were successful with > Galaxy instead, but are having trouble getting the data back into the > UCSC Browser. > > You will need to output the data in a format that meets one of the > Custom track data file format requirements. This means that it will need > at a minimum a track line and optionally a browser line. Load the data > using the Custom track submission form, the same one that you used to > load the original BAM data. Links on the submission form go to help > documents that describe formatting rules. If your data is large, > consider using a bigWig or bigBed data format. > > Custom track help, covers all types: > http://genome.ucsc.edu/goldenPath/help/hgTracksHelp.html#CustomTracks > > Double check the formatting and submission method and see if some of > this helps resolve the issue, > > Jennifer > > On 6/2/10 12:17 PM, Shashikant Pujar 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
