I don't completely understand how the paired end mode works. I want to count reads only when both the read and its mate map to the same gene. Here's what I did.
- Filtered the bam file to include only reads where the read and its mate were aligned.
- Ran featureCounts using the -p option.
Consider these cases.
a. Both the read and and its mate map to the same gene. This is counted and is what I want.
b. The read maps to one gene and its mate maps to another gene. Is this counted? Is it counted for both genes?
c. The read maps to one gene and its mate doesn't overlap any feature in the gtf file. Is this counted. once or not at all?
Thanks for your help.