When I use either option –s or –S ,  then I get the same number of counts.

I would expect that the number of counts would be different when the

Minus or plus strand is designated? 

Are these options working?

bedtools coverage -abam   -s   -a File.bam -b mm10_all.bed  > File_out.txt


Lana Schaffer

The Scripps Research Institute

Biostatistics, Informatics

DNA Array Core Facility