Answers.Body: <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>
  
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2019-11-25T08:37:04.270Z
Answers.Text: i used bam files in case of bed files but yes the orders are same .But would that help me in annotating the region ?
Answers.UserDisplayName: kcm
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Answers.CreationDate: 2019-11-25T08:45:20.463Z
Answers.Text: I assume you used `multiBamSummary BED-file`, did you use `multiBamSummary bins` instead?
Answers.UserDisplayName: Devon Ryan
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Answers.CreationDate: 2019-11-25T08:49:30.853Z
Answers.Text: "multiBamSummary bins" yes that is what i used what i saw in the manual
Answers.UserDisplayName: kcm
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2019-11-25T08:55:34.277Z
Answers.Text: They're bins of the size you specified that tile the genome then.
Answers.UserDisplayName: Devon Ryan
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2019-11-25T08:57:31.327Z
Answers.Text: okay.Now any way to annotate those regions ? the intervals which i see in the output ,as i would like to take that for downstream analysis where i would like to see the gene name
Answers.UserDisplayName: kcm
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2019-11-25T08:58:21.263Z
Answers.Text: Overlap/intersect them with a GTF file.
Answers.UserDisplayName: Devon Ryan
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2019-11-25T09:06:40.730Z
Answers.Text: Conceptual doubt ,would it be similar to annotating the peaks like that of homer annnotate peak function ? or I can simply map the the chromosome start end to gtf file.
Answers.UserDisplayName: kcm
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2019-11-25T10:20:09.133Z
Answers.Text: "Conceptual question" (a doubt is generally not something one "has" in English). I'd just simply map things to the GTF file.
Answers.UserDisplayName: Devon Ryan
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2019-11-25T11:46:03.740Z
Answers.Text: thank you @Devon clarifying my question and the English
Answers.UserDisplayName: kcm
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2019-11-25T08:28:24.343Z
Answers.LastActivityDate: 2019-11-25T08:28:24.343Z
Answers.UserDisplayName: Devon Ryan
Body: <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>
  
Tags: <deeptools>
Title: multiBamSummary output chromosome region annotate issue
ThreadText: # multiBamSummary output chromosome region annotate issue
  
  (Asked by: username_0 on 2019-11-25)
  
  I was looking how to take readcount from ATAC seq data , this [post](https://www.biostars.org/p/320394/#409383) 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
  
  **Tags:** deeptools
  
  
  ---
  
  ## 1 answers
  
  ### Answer by username_1 on 2019-11-25. Score: 2 | Accepted answer
  
  Assuming you used a BED file as input then the output is in the same order, so just merge the two files together.
  
  > **Comments:**
  > **username_0**: i used bam files in case of bed files but yes the orders are same .But would that help me in annotating the region ?  
  > **username_1**: I assume you used `multiBamSummary BED-file`, did you use `multiBamSummary bins` instead?  
  > **username_0**: "multiBamSummary bins" yes that is what i used what i saw in the manual  
  > **username_1**: They're bins of the size you specified that tile the genome then.  
  > **username_0**: okay.Now any way to annotate those regions ? the intervals which i see in the output ,as i would like to take that for downstream analysis where i would like to see the gene name  
  > **username_1**: Overlap/intersect them with a GTF file.  
  > **username_0**: Conceptual doubt ,would it be similar to annotating the peaks like that of homer annnotate peak function ? or I can simply map the the chromosome start end to gtf file.  
  > **username_1**: "Conceptual question" (a doubt is generally not something one "has" in English). I'd just simply map things to the GTF file.  
  > **username_0**: thank you @username_1 clarifying my question and the English  
  
  ---
  
  