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Old 05-10-2011, 10:31 AM   #1
Location: west coast

Join Date: May 2011
Posts: 17
Default converting bam files to non-normalized read counts

I am new to this business, so I would like to apologize in advance if this is trivial.

I have bam files produced to Tophat and need to run a differential gene expression analysis. I can do that with Cufflinks, but I also would like to compare the results with e.g. edgeR. However edgeR uses the raw counts, not normalized FPKMs. I can naively convert FPKMs to counts by multiplying to the gene length and total reads, but is there a better way to convert bam files to non-normalized read counts?
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