ChIP-seq Analysis
Overview
Chromatin immunoprecipitation sequencing (ChIP-seq) is used to analyze protein interactions with DNA. It combines chromatin immunoprecipitation (ChIP) with massively parallel DNA sequencing to identify the binding sites of DNA-associated proteins.
parse2wig
parse2wig is a tool for converting aligned read files to wiggle format, which is useful for visualization in genome browsers.
3. Peak Calling
Peak calling is a crucial step in ChIP-seq analysis, identifying regions of the genome where proteins of interest are bound. Several tools are available:
| Tool | Description | Source |
|---|---|---|
| MACS2[^1] | Model-based Analysis of ChIP-Seq. Captures local biases in sequencing data and models peak shape to improve accuracy. | GitHub |
| IDR[^2] | Irreproducible Discovery Rate. Assesses reproducibility of findings across replicates. | GitHub |
| phantompeakqualtools[^3] | A package for ChIP-seq quality control metrics, including strand cross-correlation. | GitHub |
4. Visualization and Analysis
DROMPA
DROMPA (DRaw and Observe Multiple enrichment Profiles and Annotation) is a comprehensive tool for easy-to-handle peak calling and visualization in ChIP-seq data analysis[^4].
Key features:
- Peak calling
- Visualization of enrichment profiles
- Annotation of peaks
- Computational analysis and validation of ChIP-seq data
| Feature | Description |
|---|---|
| Peak Calling | Identifies significant binding sites using a sliding window approach |
| Visualization | Generates publication-quality figures of ChIP-seq enrichment profiles |
| Annotation | Associates peaks with genomic features (e.g., promoters, genes) |
| Comparative Analysis | Allows comparison of multiple ChIP-seq datasets |
References
[^1]: Zhang Y, Liu T, Meyer CA, et al. Model-based Analysis of ChIP-Seq (MACS). Genome Biol. 2008;9(9):R137. PMID: 18798982
[^2]: Li Q, Brown JB, Huang H, Bickel PJ. Measuring reproducibility of high-throughput experiments. Ann Appl Stat. 2011;5(3):1752-1779. DOI: 10.1214/11-AOAS466
[^3]: Landt SG, Marinov GK, Kundaje A, et al. ChIP-seq guidelines and practices of the ENCODE and modENCODE consortia. Genome Res. 2012;22(9):1813-1831. PMID: 22955991
[^4]: Nakato R, Itoh T, Shirahige K. DROMPA: easy-to-handle peak calling and visualization software for the computational analysis and validation of ChIP-seq data. Genes Cells. 2013;18(7):589-601. PMID: 23672187
Created by Ryan D. Najac for the Palomero Lab at the Institute for Cancer Genetics.Page last updated on 2024-10-17.