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Old 03-01-2012, 02:21 AM   #1
Location: haifa israel

Join Date: Jun 2011
Posts: 62
Default How to remove reads in wrong direction from Cufflinks analysis

I am running sequencing data from a directional RNASeq protocol on bowtie (it is a bacterial genome) and then cuffdiff or cufflinks.
I occasionally see a few reads that align to the wrong direction (opposite strand). Is there any way to filter these out before I do my FPKM analysis?
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cufflinks, directionality, filter, rna-seq

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