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
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
galaxy-user mailing list galaxy-user@lists.bx.psu.edu http://lists.bx.psu.edu/listinfo/galaxy-user
Please note the graphing formats you can use at UCSC:
http://genomewiki.ucsc.edu/index.php/Selecting_a_graphing_track_data_format
bigWig format is most efficient.
--Hiram
galaxy-user@lists.galaxyproject.org