<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>

CC BY-SA 4.0
2019-11-25T08:37:04.270Z
i used bam files in case of bed files but yes the orders are same .But would that help me in annotating the region ?
kcm
CC BY-SA 4.0
2019-11-25T08:45:20.463Z
I assume you used `multiBamSummary BED-file`, did you use `multiBamSummary bins` instead?
Devon Ryan
CC BY-SA 4.0
2019-11-25T08:49:30.853Z
"multiBamSummary bins" yes that is what i used what i saw in the manual
kcm
CC BY-SA 4.0
2019-11-25T08:55:34.277Z
They're bins of the size you specified that tile the genome then.
Devon Ryan
CC BY-SA 4.0
2019-11-25T08:57:31.327Z
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
kcm
CC BY-SA 4.0
2019-11-25T08:58:21.263Z
Overlap/intersect them with a GTF file.
Devon Ryan
CC BY-SA 4.0
2019-11-25T09:06:40.730Z
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.
kcm
CC BY-SA 4.0
2019-11-25T10:20:09.133Z
"Conceptual question" (a doubt is generally not something one "has" in English). I'd just simply map things to the GTF file.
Devon Ryan
CC BY-SA 4.0
2019-11-25T11:46:03.740Z
thank you @Devon clarifying my question and the English
kcm
CC BY-SA 4.0
2019-11-25T08:28:24.343Z
2019-11-25T08:28:24.343Z
Devon Ryan
<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>

<deeptools>
multiBamSummary output chromosome region annotate issue
# 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

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## 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 @Devon clarifying my question and the English  

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