Question: got wrong reads counts from bedtools multicov(microRNA)
0
gravatar for xdkong
5.5 years ago by
xdkong0
Taiwan
xdkong0 wrote:

I used the 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 the samtools view -c, eg: I ran the command: samtools view -c mirna.sort.bam 1:1102504-1102525 The result was:444, ran the 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. 

 

ADD COMMENTlink modified 5.5 years ago • written 5.5 years ago by xdkong0
0
gravatar for xdkong
5.5 years ago by
xdkong0
Taiwan
xdkong0 wrote:

Who has used the bedtools multicov to count reads?

I found that add the parameter -D  can get a number near the number got from samtools -c. 

ADD COMMENTlink modified 5.5 years ago • written 5.5 years ago by xdkong0
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 2414 users visited in the last hour
_