I have paired-end reads from RNAseq experiments and I want to use bedtools intersect with the force “strandedness” parameter (-s). Will bedtools take into account the paired-end reads and treat them as a single event, or will get two lines of output, one for each of the two pairs?
I ran into a similar issue today. I do not have a direct answer to your question, but a work around that I found is to combine the mates into a bedpe file, which will keep the coordinates of each mate and you can parse them as needed. The advantage is it's a simple way to force the pairs as a single entry. This post is what sparked the idea. Hope this helps!
I obtained the same number of counts in the two strands, thus bedtools is not considering paired-end reads as a single event, but it assigns each read of the pair to one different strand.
I ran into a similar issue today. I do not have a direct answer to your question, but a work around that I found is to combine the mates into a bedpe file, which will keep the coordinates of each mate and you can parse them as needed. The advantage is it's a simple way to force the pairs as a single entry. This post is what sparked the idea. Hope this helps!