I have some RNA-seq bam files which I would like to submit to edgeR for differential expression analysis. My problem is how to extract the read count for each gene/exon from the bam files. I have followed what explained here "http://seqanswers.com/wiki/How-to/RNASeq_analysis" but for some reason that I could not figure out, I only get 0 for the read counts. I also tested "samtools idxstats aln.bam" but it only ruterns read counts for each chromosome not genes. So I was wondering if there is an other way for extraction of read counts from bam files? Also it would be very appreciated if you could give an idea what might have gone wrong with the other method that I used and got only 0.
Thanks in advance :)