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 ³wiggles² that accepts a ³SAM² format file and converts it to a ³wig² file. I¹ve mainly looked at wiggles-generated files in Integrated Genome Browser (bioviz.org/igb), but I¹m sure they can work fine in the UCSC browser, as well. A student who works with me made a small change to ³wiggles² 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 Associate Professor Dept. of Bioinformatics and Genomics, UNCC North Carolina Research Campus 600 Laureate Way Kannapolis, NC 28081 704-250-5750 www.transvar.org