I have paired-end ChIP-Seq data that resulted in a low amount of uniquely mapped reads. When mapping the reads PE, only a small percentage maps concordantly.
I want to check whether the reads give some biological sense. For that, I thought of mapping SE, taking the condition with the best statistics, running macs2, annotating, and seeing whether the annotations make sense.
So, I have separate files for R1 and R2 alignment.
Here it was advised to used R1 only. Why is it preferred to use R1 only rather than combine both reads?
When running macs2, is it advisable to combine both files into one? For example
macs2 -t sample_R1.bam sample_R2.bam -c control_R1.bam control_R2.bam