bedtools multicov problems:
I am counting number of mapped reads by using bedtools multicov:
bedtools multicov -s -D -bams AA.sorted.bam -bed yyy.bed > zzz_low_s.txt
Read counts for all bed file coordinates are zero.
When I use uppercase -S , there are reads in all coordinates.
bedtools multicov -S -D -bams AA.sorted.bam -bed yyy.bed > zzz_up_s.txt
When I do not use any stand option, there are reads in all coordinates, which are same number when I use uppercase -S
These coordinates have reads from both strands (I checked in IGV). Do you have any idea why lowercase s is not giving any count?