Calling narrow and broad peaks from ChIP-Seq data

Chromatin immunoprecipitation (ChIP) followed by high throughput sequencing (ChIP-Seq) is one of the widely used approaches for elucidating interactions between DNA and proteins. It is an essential tool for researchers to understand the role of transcription factors or histone modifications in gene regulation. While for most TFs, enriched regions typically form sharp peaks covering short regions of DNA, the pattern of reads for many types of histone modifications span regions of upto several hundred kilobases. In this webinar, we will demonstrate and assess the algorithms in StrandNGS for both narrow and broad peak calling. Specifically, results from using 'MACS' algorithm for detecting the FOXA1 transcription factor binding sites and from 'Find Enriched Regions' approach for detecting histone H3K36 modification regions will be discussed.