Answers.Body: <p>That's a <a href="https://en.wikipedia.org/wiki/FASTQ_format" rel="nofollow noreferrer">fastq</a> file, you will want to align it to the genome, call peaks, and then use something like <a href="http://meme-suite.org/index.html" rel="nofollow noreferrer">MEME</a> to determine binding motifs.</p>
  
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Answers.CreationDate: 2017-07-31T07:44:56.257Z
Answers.Text: how do I align it to the genome?
Answers.UserDisplayName: frosh
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Answers.CreationDate: 2017-07-31T07:49:41.890Z
Answers.Text: @frosh You need more help than a Q&A site can offer. I recommend that you attend a workshop on NGS data analysis, or find a collaborator who can do the analysis for you.
Answers.UserDisplayName: Devon Ryan
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Answers.CreationDate: 2017-07-31T08:10:55.723Z
Answers.Text: You're right. I will delete the question.
Answers.UserDisplayName: frosh
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Answers.Text: You don't need to delete it.
Answers.UserDisplayName: Devon Ryan
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Answers.CreationDate: 2017-07-31T23:35:12.590Z
Answers.Text: The following mini-courses may be useful: http://rafalab.github.io/pages/harvardx.html
Answers.UserDisplayName: Alex Reynolds
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Answers.UserDisplayName: Devon Ryan
Body: <p>I have the following Chip-Seq data and could not found a description of it. Can you help me with it? More, I would like to find out the order of the nucleotides in binding regions; that is, what number they are.</p>
  
  <pre><code>@GWZHISEQ01:319:HA1NPADXX:1:1101:1182:2196 1:N:0:ACTGAT
  GGAGGAAGTGTGTTGCTGCAGACAGTAGCAACCAGACCCACACTGCGCGTA
  +
  CCCFFFFFHHFHHIJJJJIJJIIIIHGJJJJJJJCGHIJJIJJFHIIJJII
  @GWZHISEQ01:319:HA1NPADXX:1:1101:1272:2109 1:N:0:ACTGAT
  NCCACGCTAGGCTCAGCTTGTCGGCCTGGCTAAGCAGTTGCGAAAGTGCGC
  +
  #1=DDDFFHHHHHJJIJJJJJJIGEHGGJIGHJFHGJIJJJJJJJ@CHCBG
  @GWZHISEQ01:319:HA1NPADXX:1:1101:1418:2141 1:N:0:ACTGAT
  GCACGCACTACCCAGAGATCATCCAAAGCCTGAAGCCACAGGGCGCACTCG
  +
  CCCFFFFFGHGHHJJJIIJJJJIIHGGGIJIIJJIIIJJJIJJJIJIJIJH
  @GWZHISEQ01:319:HA1NPADXX:1:1101:1302:2160 1:N:0:ACTGAT
  ACACTCTTTCCCTACACGACGCTCTTCCGAGATCGGAAGAGCACACGTCTG
  +
  CCCFFFFFHDHHHJJJJIJJJJIIIIIJIHJIJJJIIJHIIJJJJJJJJHH
  </code></pre>
  
Comments.ContentLicense: CC BY-SA 3.0
Comments.CreationDate: 2017-07-31T07:51:46.180Z
Comments.Text: Cross-posted [on biostars](https://www.biostars.org/p/265387/)
Comments.UserDisplayName: Devon Ryan
Comments.ContentLicense: CC BY-SA 3.0
Comments.CreationDate: 2017-07-31T08:10:08.707Z
Comments.Text: Is that a problem?
Comments.UserDisplayName: frosh
Comments.ContentLicense: CC BY-SA 3.0
Comments.CreationDate: 2017-07-31T08:11:40.930Z
Comments.Text: It's frowned upon at the very least.
Comments.UserDisplayName: Devon Ryan
Comments.ContentLicense: CC BY-SA 3.0
Comments.CreationDate: 2017-08-04T09:19:21.593Z
Comments.Text: I would argue that cross-posting is not a problem provided you reference the cross-posts on each site.
Comments.UserDisplayName: bli
Tags: <chip-seq>
Title: Chip-Seq data description
ThreadText: # Chip-Seq data description
  
  (Asked by: username_0 on 2017-07-31)
  
  I have the following Chip-Seq data and could not found a description of it. Can you help me with it? More, I would like to find out the order of the nucleotides in binding regions; that is, what number they are.
  
  ```
  @GWZHISEQ01:319:HA1NPADXX:1:1101:1182:2196 1:N:0:ACTGAT
  GGAGGAAGTGTGTTGCTGCAGACAGTAGCAACCAGACCCACACTGCGCGTA
  +
  CCCFFFFFHHFHHIJJJJIJJIIIIHGJJJJJJJCGHIJJIJJFHIIJJII
  @GWZHISEQ01:319:HA1NPADXX:1:1101:1272:2109 1:N:0:ACTGAT
  NCCACGCTAGGCTCAGCTTGTCGGCCTGGCTAAGCAGTTGCGAAAGTGCGC
  +
  #1=DDDFFHHHHHJJIJJJJJJIGEHGGJIGHJFHGJIJJJJJJJ@CHCBG
  @GWZHISEQ01:319:HA1NPADXX:1:1101:1418:2141 1:N:0:ACTGAT
  GCACGCACTACCCAGAGATCATCCAAAGCCTGAAGCCACAGGGCGCACTCG
  +
  CCCFFFFFGHGHHJJJIIJJJJIIHGGGIJIIJJIIIJJJIJJJIJIJIJH
  @GWZHISEQ01:319:HA1NPADXX:1:1101:1302:2160 1:N:0:ACTGAT
  ACACTCTTTCCCTACACGACGCTCTTCCGAGATCGGAAGAGCACACGTCTG
  +
  CCCFFFFFHDHHHJJJJIJJJJIIIIIJIHJIJJJIIJHIIJJJJJJJJHH
  
  ```
  
  **Tags:** chip-seq
  
  > **Comments:**
  > **username_1**: Cross-posted [on biostars](https://www.biostars.org/p/265387/)  
  > **username_0**: Is that a problem?  
  > **username_1**: It's frowned upon at the very least.  
  > **username_2**: I would argue that cross-posting is not a problem provided you reference the cross-posts on each site.  
  
  ---
  
  ## 1 answers
  
  ### Answer by username_1 on 2017-07-31. Score: 4
  
  That's a [fastq](https://en.wikipedia.org/wiki/FASTQ_format) file, you will want to align it to the genome, call peaks, and then use something like [MEME](http://meme-suite.org/index.html) to determine binding motifs.
  
  > **Comments:**
  > **username_0**: how do I align it to the genome?  
  > **username_1**: @username_0 You need more help than a Q&A site can offer. I recommend that you attend a workshop on NGS data analysis, or find a collaborator who can do the analysis for you.  
  > **username_0**: You're right. I will delete the question.  
  > **username_1**: You don't need to delete it.  
  > **username_3**: The following mini-courses may be useful: http://rafalab.github.io/pages/harvardx.html  
  
  ---
  
  