View source for ChIP-Seq (application)

{{Bioinformatics application
|sw 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.
|bio domain=ChIP-seq, 
|bio method=Peak calling, Read mapping, 
|bio tech=Illumina, 
|created by=Giovanna Ambrosini, Philipp Bucher
|created at=EPFL, Ecole Polytechnique Fédérale de Lausanne, Lausanne
|maintained=Yes
|input format=SGA, FPS, BED, BAM, GFF
|output format=SGA, FPS, BED, GFF
|language=C, Perl
|library=C, Perl
|licence=GPL
|os=Linux, Mac OS X
}}
== Description ==
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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. 

The ChIP-seq server is a front-end to the ChIP-seq tools, a collection of C programs and Perl scripts which can be downloaded SourceForge.net (http://sourceforge.net/projects/chip-seq). The C programs are primarily optimized for speed. For this reason, they use their own compact format for ChIP-seq data representation called SGA.The SGA (Simple Genome Annotation) format differs in one very important aspect from similar formats such as BED or GFF: it is required to be sorted by genome positions.
SGA is a single-line-oriented and tab-delimited format with the following five obligatory fields:

        1. Sequence name (Char String), 
        2. Feature (Char String),
        3. Sequence Position (Integer), 
        4. Strand (+/- or 0),
        5. Tag Counts (Integer).

We support data upload in SGA, FPS, BED and GFF formats. FPS is the specific format used by the Signal Search Analysis server, a motif discovery platform developed by our group. Users have to pay attention that chromosomes are uniquely identified. Both the ChIP-seq and Signal Search Analysis servers use RefSeq IDs including version numbers for internal representation.
The ChIP-seq server also accepts chromosome names as spelled by the UCSC genome browser on input.

The software at the back-end of the ChIP-seq server has a modular design. Each program performs an elementary data processing step in an efficient manner. The same format, SGA, is used for input and output, making it possible to carry out complex analyses task by running several programs in a pipeline. The web server mirrors this modular design to a large extent. Generally, there is a one-to-one relationship between web forms and back-end programs. The output of one service can be used as input to another service. This interoperability extends to programs of the SSA server, as both resources share common input and output formats. By combining different programs in an innovative fashion, creative users can use run novel types of analyses not even anticipated by the developers.

The ChIP-seq server offers a rich collection of server-resident public data sets from landmark papers, which have been widely used by the bioinformatics community for benchmarking and testing new algorithms.
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