This is a test version of Biostars. For the public version, visit https://www.biostars.org.
Problems with Paired-End Data when performing counts

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?

genome rna-seq software error
• 1,593 views • link
updated by Devon Ryan Devon Ryan • written by oma219 • oma219

1 answer

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.

• 0 views • link
written by Devon Ryan Devon Ryan

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

• 0 views • link
written by oma219 • oma219

Log in to answer this question.

More posts like this