Entering edit mode
8.5 years ago
xdkong
•
0
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
Who has used the bedtools multicov to count reads?
I found that add the parameter
-D
can get a number near the number got fromsamtools -c
.