Abstract

We have developed SNP calling and allelic-specific analysis pipeline for pooled ChIP-seq data that works without pre-existing genotype information of the cell line or individual. We have used a methodology that takes into account the considerable amount of noise in ChIP-seq data sets, calculates differentially bound sites using DiffBind and allelic-specific TF binding using iASeq and generates a list of putative regulatory SNPs. We tested this pipeline using ER and FOXA1 ChIP-seq data in three breast cancer cell lines MCF7 , ZR751 and T47D and compared different approaches to our analysis. I will highlight some of the challenges encountered and report on the outcome so far.