Command line analysis of ChIP-seq results

Abstract

Among the emerging next-generation sequencing technologies, ChIP-seq provides a very important tool for functional genomics studies. From the bioinformatics point of view, ChIP-seq analysis involves more than simply aligning the short reads to the reference genome. It also completes several other downstream steps, like determination of peaks, motif finding and gene ontology enrichment calculation. For these, several programs, applications and packages are available, both free and commercial. In this article I am showing the usage of two free ChIP-seq analysis packages, the HOMER and ChIPseeqer along with the MACS and MEME programs. I also provide a customisable script suitable for the complete analysis of raw ChIP-seq sequencing data either from a sequence read repository or directly from sequencing.