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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.
Users can analyse their own data by uploading mapped sequence tags in various formats, including BED and BAM.
The server also provides access to hundreds of publicly available data sets such as ChIP-seq data, RNA-seq data (i.e. CAGE), DNA-methylation data, sequence annotations (promoters, polyA-sites, etc.), and sequence-derived features (CpG, phastCons scores).

The source code is available on

The ChIP-Seq Tools

  • ChIP-Cor: Generation of an aggregation plot (feature correlation plot) for specific genomic features.

  • ChIP-Extract: Extraction of specific genome annotation features around reference genomic anchor points. The output is a table with rows representing each reference anchor point and columns the feature tag occurence at specific distances. This table can be used to generate heatmaps.

  • ChIP-Center: Read tag shifting to estimated center-positions of DNA fragments.

  • ChIP-Peak: Narrow peak caller that uses a fixed width peak size.

  • ChIP-Part: Broad peak caller algorithm used for broad regions of enrichment found in ChIP-seq experiments targeted at histone marks.

  • ChIP-Track: Generation of UCSC Genome Browser annotation tracks for data visualization.

  • ChIP-Convert: Format conversion tool for BED, BAM, SGA, and other data formats. Data export from our local data repository, the Mass Genome Annotation (MGA) database, is also available.

Acces to the Mass Genome Annotation (MGA) database

  • MGA-Search: Fast full-text search of our local collection of publicly available datasets.

You find our on-line Tutorial Series here.

Please cite us using the following reference:

  • Ambrosini, G., Dreos, R., Kumar, S., and Bucher, P. BMC Genomics (2016) 17: 938.
    The ChIP-Seq tools and web server: a resource for analyzing ChIP-seq and other types of genomic data
Last update September 2021