Hi everyone,
I'm using Illumina RNAseq to test for differential expression between two conditions. I have successfully mapped reads with tophat/bowtie, and used cufflinks/cuffcompare to test for differential expression.
A number of methods (edgeR, DEGseq, DESseq), however, ask for raw read counts rather FPKM.
Is there an easy way to go from tophat output (say the bedgraph or .sam) to raw read counts for each transcript (say using a gtf that I would supply)?
Thanks!
I'm using Illumina RNAseq to test for differential expression between two conditions. I have successfully mapped reads with tophat/bowtie, and used cufflinks/cuffcompare to test for differential expression.
A number of methods (edgeR, DEGseq, DESseq), however, ask for raw read counts rather FPKM.
Is there an easy way to go from tophat output (say the bedgraph or .sam) to raw read counts for each transcript (say using a gtf that I would supply)?
Thanks!
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