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Old 09-06-2012, 09:06 AM   #1
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Location: Manchester, UK

Join Date: Jul 2011
Posts: 5
Default Sliding window/genome coverage from pileup files?

I have SOLiD whole genome sequence data from different yeast strains (S. cerevisiae) that have been processed using samtools.

I have used samtools pileup and have .pileup file for all my yeast strains (10 column pileup format).

I would like to visualise/work out (say, maybe with a sliding window approach) not only the % genome coverage (compared to the standard S288C S. cerevisiae reference sequence) but also where the coverage is and what read depth.

Does anyone have any suggestions?

Thanks in advance
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