Hi, I have bam files for paired-end sequencing from the Hi-C experiment. I want to know the fraction of read pair orientation as a function of mapping distance. May I ask if there is software for this?
If not, I first need to extract different read pair orientations (forward-reverse, forward-forward, reverse-forward, reverse-reverse). May I ask if is a way to do this? Thanks.
Thanks! So this command extracts reverse-forward pairs?
reverse R1, forward R2
Thank you! I used the command. However, I found the output reads are not paired. The inputs are all paired. All reads are supposed to be paired, I think?
Sorry, I think the read number should be even since all the reads are in pairs but now it's an odd number. I think read 1 and read 2 should be discarded together according to the command?