I used bedtools multicov to count the number of reads in the regions of a bed file. But I think the results were wrong, like:

1   17369     17436     0
1   17409     17431     0
1   17369     17391     0
1   30366     30503     0
1   30438     30458     0
1   567705    567793    4
1   567762    567783    2
1   1102484   1102578   8
1   1102504   1102525   4
1   1102540   1102561   4

I get another number by samtools view -c, e.g., I ran the command: samtools view -c mirna.sort.bam 1:1102504-1102525 The result was 444, ran samtools view -c mirna.sort.bam 1:1102540-1102561 and got 2310, I don't know why bedtools got so small numbers, who know the reason?

Thank you