Hi, I am trying to extract expression counts from some bam files. When I used bedtools to do so, I got all 0 for every specified region (in bed file). But when I used samtools, the counts were there.
For bedtools, the code is following:
bedtools multicov -bams in.bam -bed annotation.bed | head -3
0 1 17578815 17609595 LAP3 0 1 1 201980827 202041410 CFLAR 0 2 1 45429998 45590913 LARS2 0
For samtools, I used
samtools view -c in.bam chr1:17578815-17609595
and the result I got is 24, and for the other two regions, I got 11 and 5147 respectively.
So I am wondering that what I was doing wrong? Or which result should I trust?