multiBamSummary output chromosome region annotate issue I was looking how to take readcount from ATAC seq data , this post which suggested to use bedtools and featurecounts to take out readcounts .But multiBamSummary seems to be pretty straight forward. Now I have my count file but only issue is there are no gene names. So now is it possible to annotate these chromosome regions? if so how ?

Any suggestion or help would be highly appreciated
Assuming you used a BED file as input then the output is in the same order, so just merge the two files together.