Merge regions in bedtools genomecov/bedgraph file

Merge regions in bedtools genomecov/bedgraph file


I want to calculate the number of reads mapping to regions of the genome, and I want to group these reads into bins of say 1kb. I have used bedtools genomecov to generate a bedgraph file that shows the coverage of reads across the genome.

bedtools genomecov -bg -ibam file.bam >Coverage.bedgraph

I then merged nearby regions of coverage using:

bedtools merge -d 1000 -c 4 -o sum -i Coverage.bedgraph > Coverage.merged.bedgraph

The problem is that the “sum” part adds the coverage from the different regions, so when merged, reads are counted more than once.

Is there a way to merge the regions without counting reads more than once? I think the necessary information from the bam file is probably lost at this point. Is there a way to do this with an option in bedtools genomecov i.e. can you make it report regions of coverage with a specified ‘bin’ size?




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