As already described in Chap. 7, you first have to transform your ChIP-Seq data
(unaligned .bam) into .fastq file format. First, change your working directory to the folder
where your raw sequencing data are located:
In general, ChIP-Seq is performed by sequencing 50 bp single end, thus the command to
generate .fastq files is:
In a next step, quality control can be performed on the generated *.fastq files by the
FastQC tool (https://www.bioinformatics.babraham.ac.uk/projects/fastqc/):
The output of
is an html file and can be opened using any Internet browser. For
a detailed description of FastQC Report see Sect. 7.3.1.
Fig. 12.3 Gel images of the QC steps obtained from the Agilent 2200 TapeStation system for
genomic DNA, purified, sheared DNA, and a NGS library as analyzed on the Genomic DNA, D1000,
and High Sensitivity D1000 ScreenTape, respectively. The gel images show high-quality samples.
(source: modified according to https://www.agilent.com/cs/library/applications/5991-3654EN.pdf)
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