Is there a simple way to count the number of reads that map to known exons (or genes) given a SAM file with aligned reads and an annotation GTF file?
I am aware of HTSeq, but I am not sure I am getting what I'm looking for.
For example, if I run the following:
htseq-count -m intersection-strict accepted_hits.sam mm9_ucsc_exon.gtf
I get a count of 3 for a gene that by visual inspection has many more reads mapped to it.
Any suggestion?
Thanks.
I am aware of HTSeq, but I am not sure I am getting what I'm looking for.
For example, if I run the following:
htseq-count -m intersection-strict accepted_hits.sam mm9_ucsc_exon.gtf
I get a count of 3 for a gene that by visual inspection has many more reads mapped to it.
Any suggestion?
Thanks.
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