What is deepTools?
deepTools is a suite of user-friendly tools for the visualization, quality control and normalization of data from deep-sequencing 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).
What can deepTools do?
deepTools can be installed either as a stand-alone command line application or as a Galaxy tool. To see a live version of deepTools visit our public server: http://deeptools.ie-freiburg.mpg.de.
More information about the (straight-forward!) installation via pypi or the Galaxy toolshed can be found in our Documentation.
deepTools' strength lies in the visualization of global signal patterns from deep-sequencing data using heatmaps and summary plots. Images like the following in which the output is clustered using k-means and sorted by gene length (left) or by mean score (right) are very easy to generate:
deepTool commands to generate the left heatmap:
$ computeMatrix reference-point --scoreFile Pol_II.bigwig --regionsFile genes.bed --beforeRegionStartLength 500 --afterRegionStartLength 2000 -out matrix_PolII.tab.gz $ heatmapper -m matrix_PolII.tab.gz --sortUsing region_length --kmeans 2
deepTools goes beyond visualization and contains all the required modules to process mapped reads into data formats amenable for interpretation. For example, deepTools contains modules for revising the GC bias of the sequenced data and the means to correct them. It also incorporates modules to compute the non-trivial signal vs. control ratios with several normalization methods.
To help users get started, deepTools has a large collection of tutorials, examples, a glossary and a comprehensive manual - all of this can be found in our WIKI. Our documentation not only guides the use of deepTools but also shows the steps of deep-sequencing data processing (e.g. using example workflows and describing common pitfalls.
Need help with troubleshooting?
The original publication - please cite when using deepTools:
Fidel Ramírez, Friederike Dündar, Sarah Diehl, Björn A. Grüning, and Thomas Manke. deepTools: a flexible platform for exploring deep-sequencing data Nucl. Acids Res. first published online May 5, 2014 doi:10.1093/nar/gku365
Where deepTools are used:
- DEEP consortium
- public Galaxy instance hosted by the Max-Planck-Institute for Immunobiology and Epigenetics: deeptools.ie-freiburg.mpg.de
- in-house Galaxy instance of the Max-Planck-Institute for Immunobiology and Epigenetics
- Galaxy instance of the University of Freiburg, Germany
- Galaxy instance of the ICGMB, Strasbourg, France
- Galaxy instance of LCSB and HPC @ Uni.lu, Belval, Luxembourg
Publications with deepTools-based analyses
Check here. If you know of a publication that used deepTools or our Galaxy instance, just drop us a line.