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deepTools addresses the challenge of handling the large amounts of data that are now routinely generated from DNA sequencing centers. deepTools contains useful modules to process the mapped reads data for multiple quality checks, creatingnormalized coverage files in standard bedGraph and bigWig file formats, that allow comparison between different files (for example, treatment and control). Finally, using such normalized and standardized files, deepTools can create many publication-readyvisualizations to identify enrichments and for functional annotations of the genome.

For support or questions please post toBiostars. For bug reports and feature requests please open an issueon github.

Ramírez F, Ryan DP, Grüning B, Bhardwaj V, Kilpert F, Richter AS, Heyne S, Dündar F, Manke T.deepTools2: a next generation web server for deep-sequencing data analysis. Nucleic Acids Research. 2016 Apr 13:gkw257.

Ourdocumentation contains more details on theindividual tool scopes and usages and anintroduction to our deepTools Galaxy web server includingstep-by-step protocols.

Please see also theFAQ, which we update regularly.OurGallery may give you some more ideas about the scope of deepTools.

For more specifictroubleshooting, feedback, and tool suggestions, please postto Biostars.

deepTools are available for:

• Command line usage (via pip / conda / github)
• Integration into Galaxy servers (via toolshed/API/web-browser)

There are many easy ways to install deepTools. More details can be foundhere.

In Brief:

Install through pypi

$ pip install deeptools

Install via conda

$ conda install -c bioconda deeptools

Install by cloning the repository

$ git clone https://github.com/deeptools/deepTools$ cd deepTools$ pip install .

deepTools can be easily integrated intoGalaxy. Please see theinstallation instructions in our documentation for further details.

Note: From version 2.3 onwards, deepTools supportpython3.

This tool suite is developed by theBioinformatics Facility at theMax Planck Institute for Immunobiology and Epigenetics, Freiburg.

Documentation |deepTools Galaxy |FAQ