Understand Bedtools coverage output
0
0
Entering edit mode
2.3 years ago
ramshahaya ▴ 10

I had used bedtools to check coverage.

bedtools coverage -b interval_list.bed -abam fixed.bam -d > bedtools_cov.txt
head -n 2 bedtools_cov.txt 
10  77  112 E00591:309:H7L2KCCX2:6:2215:25712:46630/2   35  -   77  112 0,0,0   1   35, 0,  1   0
10  77  112 E00591:309:H7L2KCCX2:6:2215:25712:46630/2   35  -   77  112 0,0,0   1   35, 0,  2   0

I would like to know which column in the above is for coverage information?

I would like to check coverage for my dataset.

Bedtools coverage • 487 views
ADD COMMENT

Login before adding your answer.

Traffic: 2309 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6