After quality check, the sequencing data can be mapped to the reference genome. In
terms of ChIP-Seq data a fast and sensitive alignment tool like Bowtie2 [6] is a suitable
choice (see Sect. 9.2.3.3).
One possible mapping command is:
Description of parameters:
-x
Index filename prefix (minus trailing .X.bt2)
-p
number of alignment threads to launch
-un
will output unaligned reads
-name
path/outputfile name w/o extension
Fig. 12.4 A schematic representation of the various steps and tools involved in the described ChIPSeq analysis strategy
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M. Kappelmann-Fenzl