Hello all,
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!
What is the command you are using with bedtools? Can you provide an example of the output you are getting, and the output you want?
Sounds like featureCounts can do what you want, anyway.