I have a question using bedtools with paired-end stranded RNA-seq data. Since one read is on the forward direction, and the second read is in the reverse direction, how does bedtools coverage handle these paired-reads when running it with the "-s" flag. For example, I am interested in getting coverage of a gene in a strand specific manner. Does bedtools using the paired read information. from what I can tell, it is handling each read separately, and only considering the read that is on the same strand as the gene of interest. Am I correct in assuming this? If so, then it would only count half the reads
for clarity, here is my command line that I have run:
./bedtools coverage -a MyGenes.bed -b MyMappings.bam -s -split > outfile.txt
Any thoughts would be appreciated.