ChIP-Seq (application)
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Application data |
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| Created by | Giovanna Ambrosini, Philipp Bucher |
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| Biological application domain(s) | Bioinformatics Applications |
| Principal bioinformatics method(s) | Read Mapping and Tag Distribution Analysis |
| Technology | Sanger, Illumina, 454, SOLiD |
| Created at | EPFL, Ecole Polytechnique Fédérale de Lausanne, Lausanne |
| Maintained? | Yes |
| Input format(s) | SGA, FPS, BED, BAM and GFF formats |
| Output format(s) | SGA, FPS, BED, and GFF formats |
| Programming language(s) | C, Perl |
| Software libraries | C, Perl |
| Licence | GNU Public Licence |
| Operating system(s) | Linux, Mac OS X |
Summary: The ChIP-Seq web server provides access to a set of useful tools performing common ChIP-Seq data analysis tasks, including positional correlation analysis, peak detection, and genome partitioning into signal-rich and signal-poor regions. It is an open system designed to allow interoperability with other resources, in particular the motif discovery programs from the Signal Search Analysis (SSA) server.
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Description
The ChIP-Seq server offers three main programs: ChIP-Peak, ChIP-Part, and ChIP-Cor. The first two serve to detect signal-enriched regions. The main difference between ChIP-peak and ChIP-Part lies in the output formats. ChIP-peak returns peak center positions and is typically used for detecting transcription factor binding sites. ChIP-part returns a list of signal-enriched regions defined by start and end positions. It is more useful for analyzing the genomic distribution of epigenetic marks such as histone modification marks, especially those that spread over large regions (e.g. H3K36me3). The most versatile tool is ChIP-cor, which produces a positional correlation diagram for two genomic features. Input features may be ChIP-Seq tag positions, peaks found by ChIP-peak, or any type of genome annotation that can be mapped to a single base on a chromosome.
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