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Chromatin immunoprecipitation coupled with massively parallel sequencing (ChIP-seq) is becoming increasingly popular as a method to obtain a high-resolution map of transcription factor binding sites across the genome, as well as histone modifications. In today's class, we will discuss ChIP-seq analysis of a transcription factor, although the principles are largely the same when analyzing histone modifications.
It is assumed that you are comfortable working in the command line environment. An understanding of chromatin immunoprecipitation is also useful in understanding how peak calling works. Finally, it is assumed that everyone is able to perform sequence alignment using bowtie2. For that reason, we will not be going through the alignment and instead be providing everyone with the aligned reads as the starting point for today's practical. {: .prereq}
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