Bedtools genomecov option to keep columns 4-6?
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
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rioualen
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rioualen
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Hi, Did you ever figure this issue out? I'm having the same issue with my normalization with my spike-in using genomecov. It writes over my 4th column and deletes column 5 and 6 in my bed files, of which column 6 is my strand information which is important.
Thanks!