Problems with Paired-End Data when performing counts

Question

[oma219]

I have paired end data and the pair reads aren't next to each other in the file. When I ran it with featureCounts, it gave me an error saying they weren't next to each other. I know that htseq-count expects the pairs to be next to each other, is there a way to rearrange the reads so it can work with htseq counts?

Answer 1

[Devon Ryan]

samtools sort -n. Having said that, featureCounts can be told that the input isn't query sorted and I think even htseq-count can handle that these days if you tell it to.

[oma219]

Do you know if the repair utility part of the featureCounts does that as well? I just wanted to check.