Bioinformatics CH391 Spring 2011 Final Project

Global analysis of ChIP-seq data

Daechan Park and Jagannath Swaminathan

The sequence data obtained from massive parallel sequencing following chromatin immunoprecipitation (ChIP-seq), was analysed to identify genomic regions that are the binding site of SWI6 transcription factor in Saccharomyces cerevisiae. Various algorithms are available to identify peaks (peak calling) from the background sequencing reads. The selection of the algorithms considerably affects the specificity of the results. We compared the performances of three widely used softwares - QuEST, MACS, and CisGenome, on our dataset and visualized probable binding sites. Although by comparitive analysis we wanted to boost the accuracy of our prediction, the result (or lack of it) has enabled us to question the noise in the dataset or the problem in the nature of protein pull down.