<p>The problem was that I was using wrong files. I ran a pipeline from <a href="http://code.databio.org/PEPATAC/" rel="nofollow noreferrer">here</a> and it generates several folders with many files. The <code>.bam</code> files that should be used are located in the <code>aligned_mm10</code> folder and are with the extension: <code>.pe.q10.sort.rmdup.bam</code>.</p>

CC BY-SA 4.0
2018-08-18T12:02:14.483Z
This link leads to a page not found. What was the pipeline that you were using?
llrs
CC BY-SA 4.0
2018-08-18T23:44:59.953Z
I see, it is just a `private` page, so that is why you might not be able to access it. It is this one: https://github.com/databio look for `pepatac`. Then, my answer is useless since no one can access it anyway...
Nikita Vlasenko
CC BY-SA 4.0
2018-08-17T19:07:31.357Z
2018-12-14T14:56:45.657Z
2018-12-14T14:56:45.657Z
Nikita Vlasenko
<p>I am trying to use <code>DiffBind</code> for my <code>ATACseq</code> experiment going through the <code>vignette</code> for <code>DiffBind</code>. I was able to import the data and make a heatmap with <code>plot(data)</code>. But somehow calling <code>data &lt;- dba.contrast(data, categories=DBA_TISSUE)</code> function is not working for me giving a warning message:</p>

<blockquote>
  <p>Warning message:
  Model must include count data for contrasts. </p>
</blockquote>

<p>I tried running beforehand: <code>data &lt;- dba.count(data)</code> but it is giving an error:</p>

<blockquote>
  <p>Error: Error processing one or more read files. Check warnings().
  In addition: Warning messages:
  1:<br>
  2:<br>
  3:<br>
  4:<br>
  5:<br>
  6:<br>
  7:  </p>
</blockquote>

<p>My <code>sample_sheet.csv</code>looks like that:</p>

<p><a href="https://i.sstatic.net/rlftk.png" rel="nofollow noreferrer"><img src="https://i.sstatic.net/rlftk.png" alt="enter image description here"></a></p>

<p>I just need to compare <code>Dura</code> vs <code>Microglia</code> which is <code>Tissue</code> column. How could this error be fixed? Any suggestions would be greatly appreciated.</p>

CC BY-SA 4.0
2018-08-14T08:55:38.147Z
Note that you have a BED file in the bamReads column rather than the BAM file that you fed to MACS2...
Devon Ryan
CC BY-SA 4.0
2018-08-14T15:25:55.760Z
I know but it is written in the documentation that both bed and bam files are fine. I tried supplying bam files too since I have them, but it does not work either.
Nikita Vlasenko
CC BY-SA 4.0
2018-08-14T18:33:40.787Z
Sure it can accept BED files, but they need to be from something like `bedtools bamtobed`. What was the error when you used BAM files?
Devon Ryan
CC BY-SA 4.0
2018-08-14T21:30:46.863Z
Wrong suffix error and just empty warnings as shown at the top. My data quality is poor (low mapping rates), so can it just be data quality issue?
Nikita Vlasenko
CC BY-SA 4.0
2018-08-14T22:05:43.200Z
Could be. You might try CSAW instead, it's what we use for differential accessibility with ATAC-seq data.
Devon Ryan
CC BY-SA 4.0
2018-08-15T16:01:41.510Z
Can you provide some reproducible data to test and see how to avoid the error?
llrs
CC BY-SA 4.0
2018-08-15T19:38:53.073Z
With the data that I have now it is definitely not working, and the issue is not yet solved either because of the poor quality data, or because something else is going wrong. I will post the answer if I figure out why that was happening. Besides, I am not sure how I can attach `12` files here, or even just `2` for `1` sample.
Nikita Vlasenko
CC BY-SA 4.0
2018-08-15T22:28:21.193Z
Ah, I have definitely run into this issue before - it is resolveable, but I cannot for the life of me remember exactly what the issue was. I think it was related to the file paths, but your data quality is likely not the issue.
Jared Andrews
<atac-seq>
DiffBind: Model must include count data for contrasts.
# DiffBind: Model must include count data for contrasts.

(Asked by: username_0 on 2018-08-14)

I am trying to use `DiffBind` for my `ATACseq` experiment going through the `vignette` for `DiffBind`. I was able to import the data and make a heatmap with `plot(data)`. But somehow calling `data <- dba.contrast(data, categories=DBA_TISSUE)` function is not working for me giving a warning message:

> Warning message:
> Model must include count data for contrasts.

I tried running beforehand: `data <- dba.count(data)` but it is giving an error:

> Error: Error processing one or more read files. Check warnings().
> In addition: Warning messages:
> 1:  
> 2:  
> 3:  
> 4:  
> 5:  
> 6:  
> 7:

My `sample_sheet.csv`looks like that:

[![enter image description here](https://i.sstatic.net/rlftk.png)](https://i.sstatic.net/rlftk.png)

I just need to compare `Dura` vs `Microglia` which is `Tissue` column. How could this error be fixed? Any suggestions would be greatly appreciated.

**Tags:** atac-seq
> **Comments:**
> **username_1**: Note that you have a BED file in the bamReads column rather than the BAM file that you fed to MACS2...  
> **username_0**: I know but it is written in the documentation that both bed and bam files are fine. I tried supplying bam files too since I have them, but it does not work either.  
> **username_1**: Sure it can accept BED files, but they need to be from something like `bedtools bamtobed`. What was the error when you used BAM files?  
> **username_0**: Wrong suffix error and just empty warnings as shown at the top. My data quality is poor (low mapping rates), so can it just be data quality issue?  
> **username_1**: Could be. You might try CSAW instead, it's what we use for differential accessibility with ATAC-seq data.  
> **username_2**: Can you provide some reproducible data to test and see how to avoid the error?  
> **username_0**: With the data that I have now it is definitely not working, and the issue is not yet solved either because of the poor quality data, or because something else is going wrong. I will post the answer if I figure out why that was happening. Besides, I am not sure how I can attach `12` files here, or even just `2` for `1` sample.  
> **username_3**: Ah, I have definitely run into this issue before - it is resolveable, but I cannot for the life of me remember exactly what the issue was. I think it was related to the file paths, but your data quality is likely not the issue.  

---

## 1 answers

### Answer by username_0 on 2018-08-17. Score: 0

The problem was that I was using wrong files. I ran a pipeline from [here](http://code.databio.org/PEPATAC/) and it generates several folders with many files. The `.bam` files that should be used are located in the `aligned_mm10` folder and are with the extension: `.pe.q10.sort.rmdup.bam`.

> **Comments:**
> **username_2**: This link leads to a page not found. What was the pipeline that you were using?  
> **username_0**: I see, it is just a `private` page, so that is why you might not be able to access it. It is this one: https://github.com/databio look for `pepatac`. Then, my answer is useless since no one can access it anyway...  

---

