bedtools multicov problem

Question

[Seq225]

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?

[ATpoint]

Can you post a subset of the BED file. I would guess that either the BED has "*" or "." in the strand column or no strand column at all. Therefore, neither "+", nor "-" would be specified and your result.