How to write featureCounts command for paired end RNA seq data

Question

[amira_abdulfata7]

I have 2 bam files, one for R1 and one for R2, how should I write the featureCounts command

[Matthias Zepper]

What have you tried already, and what was the problem?

[GenoMax]

If you are not interested in splicing then only one of the BAM files can be used for computing counts similar to having single end read data. But then only one file should to be used of the two. Otherwise remap as paired end as noted by ATPoint.

Answer 1

[ATpoint]

That is not how this goes. Paired-end data have to be aligned together (not independently) with a paired-end aware aligner that for RNA-seq should also be splice-aware (in case your species does splicing). THat could be something like STAR or Hisat2. Once that is done simply add the paired-end flag to featureCounts, iirc that is -p.