$ bedtools coverage -a A.bed -b B.bed -hist chr1 0 100 b1 1 + 0 70 100 0.7000000 chr1 0 100 b1 1 + 1 30 100 0.3000000 chr1 100 200 b2 1 - 1 100 100 1.0000000 chr2 0 100 b3 1 + 0 100 100 1.0000000 all 0 170 300 0.5666667 all 1 130 300 0.4333333

hi! could anyone comment on headers of these

i suppose, col i is chromosome, followed by start, end, score, strand, frame, mapped_bases, length of gene/transcript/exon/other genomic feature, coverage (not in %)

what about where "all" is mentioned?

what does that mean and what's the benefit?

and if i need to get coverage of only genes per sample for that i had included only the rows that have gene info only (excluding others like transcript, CDS, etc), but should include the rows where "all" is mentioned...

Regards