text: user285: 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 
  
  user77: Assuming you used a BED file as input then the output is in the same order, so just merge the two files together.
  
original_text: 285: <p>I was looking how to take readcount from ATAC seq data , this <a href="https://www.biostars.org/p/320394/#409383" rel="nofollow noreferrer">post</a> 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 ?</p>
  
  <p>Any suggestion or help would be highly appreciated </p>
   77: <p>Assuming you used a BED file as input then the output is in the same order, so just merge the two files together.</p>
  