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
