Based on the previous threads when using DESeq the reads should not be double counted. I am following pipeline for RNA-seq analysis and would like to know any suggestions/comments regarding the pipeline:


 1.  Mapping the reads using Tophat
 2.  Convert Tophat output.bam to Sam
 3.  Create bed file from Sam file
 4.  Use CoverageBed along with reference genome for counting the reads
 5.  Sum count of reads from all exons in a transcript
 6.  DESeq to analyze the counts/transcript

Thank you very much
Nirmala




	[[alternative HTML version deleted]]

