Question: Bedtools genomecov option to keep columns 4-6?
0
gravatar for rioualen
11 weeks ago by
rioualen430
France
rioualen430 wrote:

Hi, I'm using bedtools genomecov in order to get the coverage from one bedfile either with option -d (coverage per position) or -bga (bedgraph output). However my input bedfile comes in 6-column format, and the last 3 are not reported in the output files. I'd be particularly interested in keeping the score column, is there some option to do that? Thank you.

input.bed

NC_000913.3     91      5009       -      82.302  +
NC_000913.3     274     307        -      88.889  -
NC_000913.3     5320    5437       -      77.311  +
NC_000913.3     5551    5600       -      84.314  +
NC_000913.3     5556    5600       -      86.957  +
NC_000913.3     5565    5603       -      90.244  +
NC_000913.3     5565    5600       -      89.189  -

bedtools genomecov -d -i input.bed -g coli.genome

NC_000913.3     1       0
NC_000913.3     2       0
NC_000913.3     3       0
NC_000913.3     4       0
NC_000913.3     5       0
NC_000913.3     6       0

bedtools genomecov -bga -i input.bed -g coli.genome

NC_000913.3     0       91      0
NC_000913.3     91      274     1
NC_000913.3     274     307     2
NC_000913.3     307     5009    1
NC_000913.3     5009    5320    0
bedtools bed genomecov • 88 views
ADD COMMENTlink modified 11 weeks ago • written 11 weeks ago by rioualen430
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: 1354 users visited in the last hour