Probably this question has been already answered somewhere, but I do not find the answer or I am not sure if the answer is really for my question.
I would like to know the number of reads that are mapping to a region from X to Y, which at the same time has some regions between x et y? I meant, I got some transcripts regions from cufflinks and in those transcripts there are the exons. So, I would like to know the number of reads mapping the region taking into account the splice ?
So in the example above, I would like to have the answer of 4 reads. I already tried coverage form bedtools, this is giving me for each exon the number of reads, but if I take the transcript (from X to Y) in consideration the real number is gonna be duplicated.
So, anyone have an idea. Thank you in advance!