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Friederike Dündar edited this page Jan 19, 2016 · 28 revisions

For instructions on using the latest deepTools version, please go here. This page only applies to deepTools 1.5

Welcome to the deepTools wiki!

deepTools is a suite of user-friendly tools for the visualization, quality control and normalization of data from high-throughput DNA sequencing experiments.

deepTools offers multiple methods for highly-customizable data visualization that immensely aid hypothesis generation and data interpretation. It also offers all the tools needed to create coverage files in standard bedGraph and bigWig file formats allowing various normalization procedures and comparisons between two files (for example, treatment and control).

This wiki accompanies the code of deepTools that is continuously being developed and hosted here at github.

Quick navigation

Why we built the tools suite Tools for quality control Step-by-step protocols of typical deepTools applications Installing deepTools Introduction into the Galaxy framework
How we use deepTools Tools for normalization and bigWig Generation Gallery of images generated with deepTools List of all command line options for all tools FAQs
What deepTools can do Tools for visualization Glossary

How to get started?

If you are starting out with data analysis of data obtained through high-throughput sequencing (= massive parallel short read sequencing = deep sequencing = Next-Generation-Sequencing = NGS), we recommend to get familiar with deepTools and the concepts of NGS data analysis that we are incorporating (→ About deepTools, Tools Overview). Our Glossary might also be helpful in case you get lost in NGS between BAMs, inputs, bins, and bigWigs.

To get an idea of the analyses that can be performed using deepTools, please see the exemplary workflows and visit our public web server: In our Gallery we're collecting all kinds of plots that were generated using deepTools.

If you already know that deepTools is exactly what you have been looking for, the information about the Installation is probably for you.

Note that the publication of deepTools also contains a deepTools manual in pdf format.

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