Can anybody address these 3 questions in calculating counts for strand-specific by HTseq-count.
How the HTseq-count calculate counts for strand-specific RNAseq. I want to ask the principle of it.
After I checked the Refseq database, I found about 280 genes have two copies in different strand (and different location). Although most of the genes don't have this problem. While HTseq-count calculate the counts, how does it deal with this issue.
Can I compare the gene expression (rpkm or counts) from the strand-specific library and from unstranded library?
Thanks a lot!!