Hello,

My question is I use as follows

coverageBed -counts -abam "input.bam" -b "40kb.bin.bed" > out.coverage.bed

But the output is as bellow |head chr1 3000081 3000131 SRR5633684.8671454/1 11 + 3000081 3000131 0,0,0 1 50, 0, 1 chr1 3000130 3000230 SRR5633685.159807408/1 47 + 3000130 3000230 0,0,0 1 100, 0, 1

It didn;t even overlap with the 40kb bin bed which is chr1 0 40000 chr1 40000 80000

and bam is noduplicate sorted.

Why would this happen? I could not find out

I expect as bellow as output.

chr1 1040000 1080000 2222 chr1 2080000 2120000 4219

thank you