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Old 12-14-2011, 08:55 PM   #1
Pamela Mukhopadhyay
Junior Member
Location: Australia, Brisbane

Join Date: May 2010
Posts: 1
Default Add Readgroups to Tophat multiple sample input?

I have got 75bp single end RNA-seq data from 8 samples. And I would like to pool reads from multiple samples to run Tophat. The problem is, we will be running cufflinks pipeline after mapping. And cuffdiff requires bam files per sample. Is there any way I can split the bam file after Tophat run? How can I give separate Readgroup tags to each sample in my Tophat run?
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