<p>I was calling the function incorrectly. Here is how it worked:</p>

<pre><code>conclusion &lt;- atacPipe("mm10", fastqInput1 = paste0(base_folder, "Micro_atac12.fastq.gz"),
                   adapter1 = "CAAGCAGAAGACGGCATACGAGATGTAGAGAGGTCTCGTGGGCTCGGAGATGT",
                   createReport = TRUE)
</code></pre>

CC BY-SA 4.0
2018-07-17T20:07:00.087Z
2018-07-17T20:07:00.087Z
Nikita Vlasenko
<p>I have several <code>atac_seq.gz</code> files and I need to run the <a href="https://www.bioconductor.org/packages/release/bioc/html/esATAC.html" rel="nofollow noreferrer">pipeline</a> with them.</p>

<p>I have single end <code>ATACseq</code>, so the function <code>atacPipe</code> requires me to have some kind of <code>adapter sequence</code> for it to run. What is it? Where could I get one?</p>

<blockquote>
  <p>Update</p>
</blockquote>

<p>I found the adapter sequences, supplied them, but it is writing me that </p>

<blockquote>
  <p>Error in atacPipe(case = list("mm10", fastqInput1 = paste0(base_folder,  : 
    adapter1 should not be NULL for single end sequencing data</p>
</blockquote>

<pre><code>library(esATAC)
base_folder &lt;- "/Users/nikitavlasenko/Downloads/sams_dev/"
conclusion &lt;- atacPipe(case=list("mm10", fastqInput1 = paste0(base_folder, "Micro_atac12.fastq.gz"),
                   adapter1 = 
"CAAGCAGAAGACGGCATACGAGATGTAGAGAGGTCTCGTGGGCTCGGAGATGT",
                   createReport = TRUE))
</code></pre>

<p>I supplied it and it is not null, so I am not sure what I am doing wrong.</p>

CC BY-SA 4.0
2018-07-17T00:58:03.633Z
Presumably one would have to know which platform the data came from since (at least for RNA seq) there are different adapter sequence sets. [This](https://github.com/ParkerLab/bioinf525/blob/master/README.md#trimming) write up has an adapter sequence agnostic approach.
NatWH
<atac-seq>
Supplying adapter sequences for ATACseq pipeline
# Supplying adapter sequences for ATACseq pipeline

(Asked by: username_0 on 2018-07-17)

I have several atac_seq.gz files and I need to run the pipeline with them.
I have single end ATACseq, so the function atacPipe requires me to have some kind of adapter sequence for it to run. What is it? Where could I get one?

Update

I found the adapter sequences, supplied them, but it is writing me that 

Error in atacPipe(case = list("mm10", fastqInput1 = paste0(base_folder,  : 
    adapter1 should not be NULL for single end sequencing data

library(esATAC)
base_folder <- "/Users/nikitavlasenko/Downloads/sams_dev/"
conclusion <- atacPipe(case=list("mm10", fastqInput1 = paste0(base_folder, "Micro_atac12.fastq.gz"),
                   adapter1 = 
"CAAGCAGAAGACGGCATACGAGATGTAGAGAGGTCTCGTGGGCTCGGAGATGT",
                   createReport = TRUE))

I supplied it and it is not null, so I am not sure what I am doing wrong.

**Tags:** atac-seq
> **Comments:**
> **username_1**: Presumably one would have to know which platform the data came from since (at least for RNA seq) there are different adapter sequence sets. [This](https://github.com/ParkerLab/bioinf525/blob/master/README.md#trimming) write up has an adapter sequence agnostic approach.  

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## 1 answers

### Answer by username_0 on 2018-07-17. Score: 0 | Accepted answer

I was calling the function incorrectly. Here is how it worked:
conclusion <- atacPipe("mm10", fastqInput1 = paste0(base_folder, "Micro_atac12.fastq.gz"),
                   adapter1 = "CAAGCAGAAGACGGCATACGAGATGTAGAGAGGTCTCGTGGGCTCGGAGATGT",
                   createReport = TRUE)


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