Hi,

If you are mainly interested in viewing coverage, the pileup format may be overkill, since it captures base frequencies per position.

The BowTie/TopHat source code distribution includes a program called “wiggles” that accepts a “SAM” format file and converts it to a “wig” file.

I’ve mainly looked at wiggles-generated files in Integrated Genome Browser (bioviz.org/igb), but I’m sure they can work fine in the UCSC browser, as well.

A student who works with me made a small change to “wiggles” that lets you run it like so:

samtools view accepted_hits.bam | wiggles > coverage.wig

If you would like him to send it to you, let me know!

Best,

Ann Loraine


On 1/11/11 9:08 PM, "Swathi Ashok Kumar" <sak980@psu.edu> wrote:

Hi, I was wondering if you have a tool that converts pileup files to variable step wigs so I can view coverage on UCSC. At present I have a rnaseq data mapped using bowtie. I've converted them to bam and generated pileups.

thanks

-- Swathi A. Kumar
 
   Interdepartmental Program in Genetics
   Center for Comparative Genomics
   Huck Institute of Life Science
   
   email : sak980@psu.edu
   tel : +1 814 441 8120






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Ann Loraine
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Dept. of Bioinformatics and Genomics, UNCC
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