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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.
| ABOUT deepTools | THE TOOLS | EXAMPLE USAGES | TECHNICAL DOCUMENTATION | HELP |
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| 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 |
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: http://deeptools.ie-freiburg.mpg.de. 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.
- check our FAQ
- get in touch: deeptools@googlegroups.com
