Answers.Body: <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>
  
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2018-07-17T20:07:00.087Z
Answers.LastActivityDate: 2018-07-17T20:07:00.087Z
Answers.UserDisplayName: Nikita Vlasenko
Body: <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>
  
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2018-07-17T00:58:03.633Z
Comments.Text: 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.
Comments.UserDisplayName: NatWH
Tags: <atac-seq>
Title: Supplying adapter sequences for ATACseq pipeline
ThreadText: # 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](https://www.bioconductor.org/packages/release/bioc/html/esATAC.html) 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/username_0/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.  
  
  ---
  
  ## 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)
  
  ```
  
  
  ---
  
  