RSEG Software

RSEG software

The RSEG software package is aimed to analyze ChIP-Seq data, especially for identifying genomic regions and their boundaries marked by diffusive histone modification markers, such as H3K36me3 and H3K27me3. It can work with or without control sample. It can be used to find regions with differential histone modifications patterns, either comparsion between two cell types or between two kinds of histone modifications.

Readme first


Auxillary data files for using RSEG

Chromosome size files

A file with chromosome sizes is required when using RSEG. The following work for the corresponding genome builds:

Deadzone files

A file of “deadzones” is strongly recommended when using RSEG to account for mappability:

Application of RSEG to publicly available dataset

  • Epigenomic domains and boudaries in human CD4+ T cells. Click here to download the result. The domains from simulateneous analysis of H3K36me2 and H3K79me2 are downloadable from here. The original dataset is from Barski A, Cuddapah S, Cui K, Roh TY, Schones DE, Wang Z, Wei G, Chepelev I, Zhao K (2007) High-resolution profiling of histone methylations in the human genome. Cell 129:823–837.
  • Epigenomic domains and boudaries in mouse pluritotent and lineage-committed cells. Click here to download the result. The original dataset is from Mikkelsen TS, Ku M, Jaffe DB, Issac B, Lieberman E, Giannoukos G, …, Bernstein BE (2007) Genome-wide maps of chromatin state in pluripotent and lineage-committed cells. Nature 448:553–560.
  • Differential histone modification regions (DHMR) between human hetatopoietic cells and erythrocyte precursors. Click here to download the result. The original dataset is from Cui K, Zang C, Roh T, Schones D, Childs R, Peng W, Zhao K (2009) Chromatin signatures in multipotent human hematopoietic stem cells indicate the fate of bivalent genes during differentiation. Cell Stem Cell 4:80–93.

Small scale test dataset

This dataset is the Chromosome I data from the following Barski’s data.
When using this small scale test dataset, the chromosome size file is
human-hg18-chr1-size.bed and the deadzone file is deadzones-k25-hg18-chr1.bed.

Simulated test dataset

Supplementary material accompanying the RSEG paper

  • Supplementary material accompanying the RSEG paper [PDF]


The authors would like to thank Timothy Daley, Shihua Zhang, Ying Wang,
Chao Dai and Qingjiao Li for testing the RSEG software. The authors would
also like to thank Elena Harris, Philip Uren and Timothy Daley for their
help in preparing the manuscript.


Contact Dr. Andrew Smith and/or Dr. Qiang Song for any questions

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