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 samples. It can be used to find regions with differential histone modifications patterns, either comparison between two cell types or between two kinds of histone modifications.
Here is a link to the latest development branch at Github.
README
- RSEG Manual (v0.4.9) (Version 0.4.9 update of RSEG changed several command line options. Please read this updated manual if you use v0.4.9)
- RSEG Manual (v0.4.4)
Software
- Download new version of rseg (0.4.9)
- rseg (0.4.4)
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:
- Human hg18 human-hg18-size.bed
- Mouse mm9 mouse-mm9-size.bed
- Fruitfly dm3 fruitfly-dm3-size.bed
Deadzone files
A file of “deadzones” is strongly recommended when using RSEG to account for mappability:
- Human hg18 (read length 25) deadzones-k25-hg18.bed
- Human hg18 (read length 27) deadzones-k27-hg18.bed
- Human hg18 (read length 32) deadzones-k32-hg18.bed
- Human hg18 (read length 36) deadzones-k36-hg18.bed
- Human hg19 (read length 25) deadzones-k25-hg19.bed
- Human hg19 (read length 27) deadzones-k27-hg19.bed
- Human hg19 (read length 32) deadzones-k32-hg19.bed
- Human hg19 (read length 36) deadzones-k36-hg19.bed
- Human hg19 (read length 41) deadzones-k41-hg19.bed.bz2
- Mouse mm9 (read length 27) deadzones-k27-mm9.bed
- Mouse mm9 (read length 36) deadzones-k36-mm9.bed
- Fruitfly dm3 (read length 24) deadzones-k24-dm3.bed
- Fruitfly dm3 (read length 25) deadzones-k25-dm3.bed
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.
- H3K36me3, Chromosome 1, Human hg18
- H3K27me3, Chromosome 1, Human hg18
- Chromosome 1 size file
- Chromosome 1 deadzone file
Simulated test dataset
- Simulated 6000 H3K36me3 enriched regions in Mouse mm9 lib-k36-6000a.bed
- Simulated whole cell extract data in Mouse mm9 lib-control.bed
Supplementary material accompanying the RSEG paper
- Supplementary material accompanying the RSEG paper [PDF]
Acknowledgement
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.
Support
Contact Dr. Andrew Smith and/or Dr. Qiang Song for any questions
RSEG User’s mainling list: rseg-support@googlegroups.com Visit archive of this mailing list