<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>

CC BY-SA 3.0
2017-07-31T07:44:56.257Z
how do I align it to the genome?
frosh
CC BY-SA 3.0
2017-07-31T07:49:41.890Z
@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.
Devon Ryan
CC BY-SA 3.0
2017-07-31T08:10:55.723Z
You're right. I will delete the question.
frosh
CC BY-SA 3.0
2017-07-31T08:12:13.783Z
You don't need to delete it.
Devon Ryan
CC BY-SA 3.0
2017-07-31T23:35:12.590Z
The following mini-courses may be useful: http://rafalab.github.io/pages/harvardx.html
Alex Reynolds
CC BY-SA 3.0
2017-07-31T07:23:14.257Z
2017-08-04T10:20:55.950Z
2017-08-04T10:20:55.950Z
Devon Ryan
<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>

CC BY-SA 3.0
2017-07-31T07:51:46.180Z
Cross-posted [on biostars](https://www.biostars.org/p/265387/)
Devon Ryan
CC BY-SA 3.0
2017-07-31T08:10:08.707Z
Is that a problem?
frosh
CC BY-SA 3.0
2017-07-31T08:11:40.930Z
It's frowned upon at the very least.
Devon Ryan
CC BY-SA 3.0
2017-08-04T09:19:21.593Z
I would argue that cross-posting is not a problem provided you reference the cross-posts on each site.
bli
<chip-seq>
Chip-Seq data description
# 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**: @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.  
> **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  

---

