Entering edit mode
2.8 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.