deepTools2: a next generation web server for deep-sequencing data analysis
Open accessAbstract
We present an update to our Galaxy-based web server for processing and visualizing deeply sequenced data. Its core tool set, deepTools, allows users to perform complete bioinformatic workflows ranging from quality controls and normalizations of aligned reads to integrative analyses, including clustering and visualization approaches. Since we first described our deepTools Galaxy server in 2014, we have implemented new solutions for many requests from the community and our users. Here, we introduce significant enhancements and new tools to further improve data visualization and interpretation. deepTools continue to be open to all users and freely available as a web service at deeptools.ie-freiburg.mpg.de The new deepTools2 suite can be easily deployed within any Galaxy framework via the toolshed repository, and we also provide source code for command line usage under Linux and Mac OS X. A public and documented API for access to deepTools functionality is also available.
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ChIP-seq bigwigs were generated with scaling factors calculated using the formula (human reads in input) / (mouse reads in input) / (human reads in ChIP) x 15,000,000 to calibrate between mouse ESCs and human HEK spike-in.
“Bigwigs were generated with the bamCoverage function from deepTools (82) with scaling factors calculated using the formula (human reads in input) / (mouse reads in input) / (human reads in ChIP) x 15000000 (83, 84).”
From Synergy between regulatory elements can render cohesin dispensable for distal enhancer function (2026) · cites this paper as [82]
For genome-wide profiles and peak overlaps, CUT&Tag peaks were filtered for a minimum signal of 1000.
“For genome-wide profiles and peak overlaps, peaks were filtered for a minimum signal of 1000 and then generated using the plotProfile function in deepTools2 (82) centered on peaks called from control (DMSO) cells and separated by replicate.”
From Synergy between regulatory elements can render cohesin dispensable for distal enhancer function (2026) · cites this paper as [82]
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- Authors
- Ramírez, F., Ryan, D. P., Grüning, B., Bhardwaj, V., Kilpert, F., Richter, A. S., Heyne, S., Dündar, F., & Manke, T.
- Affiliations
- Max Planck Institute of Immunobiology and Epigenetics (DE)
- University of Freiburg (DE)
- Weill Cornell Medicine (US)
- Corresponding author
- Manke, Thomas
- ORCID
- Venue
- Nucleic Acids Research
- Publisher
- Oxford University Press (OUP)
- Published
- 2016-04-13
- Volume
- 44
- Issue
- W1
- Pages
- W160-W165
- ISSN
- 0305-1048 (ISSN-L)
- 1362-4962
- PMC
- PMC4987876
- OpenAlex
- W2341539131
- Cited by
- 8,096
- References
- 2
- Citations by year
- 2026: 1065 · 2025: 1325 · 2024: 1238 · 2023: 1188 · 2022: 1018 · 2021: 941 · 2020: 602 · 2019: 393 · 2018: 234 · 2017: 85 · 2016: 5 · 2012: 1
- FWCI
- 124.25
- Type
- journal article
- Language
- en
- Open access
- gold
- doi.org
- Licence
- Locations
- Nucleic Acids Research (publishedVersion, cc-by-nc)
- Europe PMC (PubMed Central) (publishedVersion, cc-by-nc)
- PubMed Central (publishedVersion, cc-by-nc)
- PubMed (publishedVersion)
- FreiDok plus (Universitätsbibliothek Freiburg) (submittedVersion, other-oa)
- HighWire Press Open Archive (submittedVersion)
- MPG.PuRe (Max Planck Society) (submittedVersion)
- Funders
- Deutsche Forschungsgemeinschaft (SFB 992)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Chromatin Dynamics
- Social Sciences › Decision Sciences › Information Systems and Management › Scientific Computing and Data Management
- Keywords
- read normalization, read quality control, read clustering, data visualization
- MeSH terms
- Animals, Base Sequence, Computer Graphics, Drosophila melanogaster, Humans, Software, Information Storage and Retrieval, Sequence Alignment, Sequence Analysis, DNA, Computational Biology, Internet, High-Throughput Nucleotide Sequencing
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