Hi All,

I want to extract the counts that are arising form pre-mRNA (i.e non-split reads). For the sigle-end library kind of easy but for the paired end the situation is bit different. Because FWD reads in the exon and reverse reads are in the introns so i don't know how to extract this information. I have searched quiet a lot but not able to find the information. My read size is 60 nt and insert size 250nt. Can some please help me with this.