DROMPA: easy-to-handle peak calling and visualization software for the computational analysis and validation of ChIP-seq data.

ABSTRACT: Chromatin immunoprecipitation with high-throughput sequencing (ChIP-seq) can identify genomic regions that bind proteins involved in various chromosomal functions. Although the development of next-generation sequencers offers the technology needed to identify these protein-binding sites, the analysis can be computationally challenging because sequencing data sometimes consist of >100 million reads/sample. Herein, we describe a cost-effective and time-efficient protocol that is generally applicable to ChIP-seq analysis; this protocol uses a novel peak-calling program termed DROMPA to identify peaks and an additional program, parse2wig, to preprocess read-map files. This two-step procedure drastically reduces computational time and memory requirements compared with other programs. DROMPA ena

SUBMITTER: Nakato R 

PROVIDER: S-EPMC3738949 | biostudies-literature | 2013 Jul

REPOSITORIES: biostudies-literature