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" <sak...@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 : sak...@psu.edu
>    tel : +1 814 441 8120
> 
> 
> 
> 
> 
> 
> 
> _______________________________________________
> galaxy-user mailing list
> galaxy-user@lists.bx.psu.edu
> http://lists.bx.psu.edu/listinfo/galaxy-user

-- 
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


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