Answers.Body: <p>Before you proceed, it is usual to do quality control on the .fastq data.  The FASTQC program is a good place to start.  </p>
  
  <p>Once you have checked the quality, trimming is the typical next step to remove low-quality data.  There are options such as Trimomatic, trimGalore for this.</p>
  
  <p>Once you are sure you have clean data, your first step is alignment - align the sequences in the .fastq file to the reference sequence in the .fasta file.  bowtie2 is one option for this process.  This gets you to the .bam stage.</p>
  
  <p>These steps will take a little time, some research, and may be somewhat frustrating, but they are the foundation for what you want to do. One option for somewhat automating these steps is to use the Galaxy platform (usegalaxy.org), otherwise these are mostly command-line tools.</p>
  
  <p>The bam to wig and wig to bigwig steps are relatively simple conversions, and Biostars has answers for these.</p>
  
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2019-08-01T14:12:05.730Z
Answers.Text: What about peak calling once I have a bigwig file?
Answers.UserDisplayName: 0x90
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2019-08-01T15:38:38.053Z
Answers.Text: I have heard of the R package BayesPeak, but ChIP-Seq is not really my thing.
Answers.UserDisplayName: Jay Moore
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2019-08-05T02:48:52.180Z
Answers.Text: macs2 should do the work.
Answers.UserDisplayName: 0x90
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2019-08-01T08:54:34.413Z
Answers.LastActivityDate: 2019-08-01T08:54:34.413Z
Answers.UserDisplayName: Jay Moore
Body: <p>I have a reference .fasta file and a raw .fastq file with chip-seq data. I am trying to create a bigwig track from the and .fastq and .fasta ref file of the raw signal. Then I would like to do some peak analysis for the chip-seq track.</p>
  
  <p>Can someone help me with googling the write things, I feel really lost while trying to google it and not sure where to start from. I was thinking to do <code>.fastq -&gt; .bam -&gt; wig -&gt; bigwig</code> and then somehow to do peak detection analysis. </p>
  
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2019-08-01T08:38:03.787Z
Comments.Text: Maybe follow some tutorials first? On [Biostars](https://www.biostars.org/p/272802/) many links to helpful tutorials.
Comments.UserDisplayName: benn
Tags: <fastq><chip-seq>
Title: How to convert a .fastq chip-seq file into a wig/bigwig track and how to extract chip-seq peaks?
ThreadText: # How to convert a .fastq chip-seq file into a wig/bigwig track and how to extract chip-seq peaks?
  
  (Asked by: username_0 on 2019-07-31)
  
  I have a reference .fasta file and a raw .fastq file with chip-seq data. I am trying to create a bigwig track from the and .fastq and .fasta ref file of the raw signal. Then I would like to do some peak analysis for the chip-seq track.
  
  Can someone help me with googling the write things, I feel really lost while trying to google it and not sure where to start from. I was thinking to do `.fastq -> .bam -> wig -> bigwig` and then somehow to do peak detection analysis.
  
  **Tags:** fastq, chip-seq
  
  > **Comments:**
  > **username_1**: Maybe follow some tutorials first? On [Biostars](https://www.biostars.org/p/272802/) many links to helpful tutorials.  
  
  ---
  
  ## 1 answers
  
  ### Answer by username_2 on 2019-08-01. Score: 1
  
  Before you proceed, it is usual to do quality control on the .fastq data. The FASTQC program is a good place to start.
  
  Once you have checked the quality, trimming is the typical next step to remove low-quality data. There are options such as Trimomatic, trimGalore for this.
  
  Once you are sure you have clean data, your first step is alignment - align the sequences in the .fastq file to the reference sequence in the .fasta file. bowtie2 is one option for this process. This gets you to the .bam stage.
  
  These steps will take a little time, some research, and may be somewhat frustrating, but they are the foundation for what you want to do. One option for somewhat automating these steps is to use the Galaxy platform (usegalaxy.org), otherwise these are mostly command-line tools.
  
  The bam to wig and wig to bigwig steps are relatively simple conversions, and Biostars has answers for these.
  
  > **Comments:**
  > **username_0**: What about peak calling once I have a bigwig file?  
  > **username_2**: I have heard of the R package BayesPeak, but ChIP-Seq is not really my thing.  
  > **username_0**: macs2 should do the work.  
  
  ---
  
  