I am using featurecounts after mapping of my reads. I have a paired-end sequencing data but Only a low percentage of reads were mapped when the paired-end reads were mapped separately and hence they were merged to a single-end read and mapped.
I know that when we use paired-end reads in featurecounts, we have to give paired-end option and also allow multi-overlap.
Does this stand true for merged single end reads too? Or should i give it as single-end read (since I have only a single bam file) and allow multi-overlaps?
The read counts are similar to ht-seq count when the multi-overlap option is set false.