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Old 06-13-2011, 10:44 AM   #1
Location: USA

Join Date: Jun 2011
Posts: 44
Default Raw read counts for RNAseq

hi All,
I want to use DESeq package for differential expression analysis.
How do I obtain the raw read counts from each of the SAM files?
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Old 06-14-2011, 11:08 AM   #2
Location: United States

Join Date: Sep 2008
Posts: 27

Check out Aaron Quinlan's bedtools. The coverageBed utility will get you what you are looking for.
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Old 06-15-2011, 05:56 AM   #3
Location: ShangHai

Join Date: Nov 2009
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htseq-count can also handle it.
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