Answers.Body: <p>The sequence to trim for ATAC-seq is <code>CTGTCTCTTATACACATCT</code>. It's the Nextera adapter sequence. The sequence is the reverse complement of the 3' ends of your primers, both forward and reverse.</p>
  <p>You trim adapters which come before any index sequence so trimming adapter (and by this everything beyond it) is sufficient.</p>
  
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Answers.CreationDate: 2023-06-14T11:31:49.710Z
Answers.LastActivityDate: 2023-06-14T20:53:22.297Z
Answers.LastEditDate: 2023-06-14T20:53:22.297Z
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Body: <p>I am just starting on my atac-seq analysis (not very experienced, so my apologies for a stupid question), and I am wanting to trim the adapters of off my paired-end reads.</p>
  <p>I am following the galaxy atac-seq protocol that says to enter in the custom 3' adapter sequence. I took the primer sequences from Buenrostro.</p>
  <pre><code>&gt;Ad1_noMX
  AATGATACGGCGACCACCGAGATCTACACTCGTCGGCAGCGTCAGATGTG
  &gt;Ad2.7_CTCTCTAC
  CAAGCAGAAGACGGCATACGAGATGTAGAGAGGTCTCGTGGGCTCGGAGATGT
  </code></pre>
  <p>Following the ATAC protocol, I see that the primer sequences they used are the reverse complement sequences of the end of the provided sequences (ACATCTCCGAGCCCACGAGAC/CACATCTGACGCTGCCGACGA). I took this part and added the reverse complement index primer of 2.7 (GTAGAGAG) to the front.</p>
  <p>So for my R1 my sequence is:
  GTAGAGAGACATCTCCGAGCCCACGAGAC
  And for my R2 my sequence is:
  GTAGAGAGCACATCTGACGCTGCCGACGA</p>
  <p>However, when I run the command I only get 1.4% read1/2 with adapter. Could anyone suggest where I am going wrong?</p>
  <p>Thank you</p>
  
Tags: <atac-seq><cutadapt><galaxy><indexing>
Title: How to identify index sequences for cutadapt for atac-seq
ThreadText: # How to identify index sequences for cutadapt for atac-seq
  
  (Asked by: username_0 on 2023-06-14)
  
  I am just starting on my atac-seq analysis (not very experienced, so my apologies for a stupid question), and I am wanting to trim the adapters of off my paired-end reads.
  
  I am following the galaxy atac-seq protocol that says to enter in the custom 3' adapter sequence. I took the primer sequences from Buenrostro.
  
  ```
  >Ad1_noMX
  AATGATACGGCGACCACCGAGATCTACACTCGTCGGCAGCGTCAGATGTG
  >Ad2.7_CTCTCTAC
  CAAGCAGAAGACGGCATACGAGATGTAGAGAGGTCTCGTGGGCTCGGAGATGT
  
  ```
  
  Following the ATAC protocol, I see that the primer sequences they used are the reverse complement sequences of the end of the provided sequences (ACATCTCCGAGCCCACGAGAC/CACATCTGACGCTGCCGACGA). I took this part and added the reverse complement index primer of 2.7 (GTAGAGAG) to the front.
  
  So for my R1 my sequence is:
  GTAGAGAGACATCTCCGAGCCCACGAGAC
  And for my R2 my sequence is:
  GTAGAGAGCACATCTGACGCTGCCGACGA
  
  However, when I run the command I only get 1.4% read1/2 with adapter. Could anyone suggest where I am going wrong?
  
  Thank you
  
  **Tags:** atac-seq, cutadapt, galaxy, indexing
  
  
  ---
  
  ## 1 answers
  
  ### Answer by username_1 on 2023-06-14. Score: 2
  
  The sequence to trim for ATAC-seq is `CTGTCTCTTATACACATCT`. It's the Nextera adapter sequence. The sequence is the reverse complement of the 3' ends of your primers, both forward and reverse.
  
  You trim adapters which come before any index sequence so trimming adapter (and by this everything beyond it) is sufficient.
  
  
  ---
  
  