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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.

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  • $\begingroup$ Maybe follow some tutorials first? On Biostars many links to helpful tutorials. $\endgroup$
    – benn
    Aug 1 '19 at 8:38
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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.

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  • $\begingroup$ What about peak calling once I have a bigwig file? $\endgroup$
    – 0x90
    Aug 1 '19 at 14:12
  • $\begingroup$ I have heard of the R package BayesPeak, but ChIP-Seq is not really my thing. $\endgroup$ Aug 1 '19 at 15:38
  • $\begingroup$ macs2 should do the work. $\endgroup$
    – 0x90
    Aug 5 '19 at 2:48

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