DeepTools
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Application data |
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| Created by | Fidel Ramírez, Friederike Dündar, Björn Grüning, Sarah Diehl, Thomas Manke |
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| Biological application domain(s) | Genomics, ChIP-seq |
| Principal bioinformatics method(s) | Standardisation and normalisation, Visualisation, Conversion |
| Technology | Illumina HiSeq, 454, Illumina |
| Created at | deepTools is maintained by the Bioinformatics and Deep-Sequencing Unit at the Max Planck Institute of Immunobiology and Epigenetics. |
| Maintained? | Yes |
| Input format(s) | bed, bam, sam, BEDGraph, BedGraph, BigWig |
| Output format(s) | bed, bam, sam, BEDGraph, BedGraph, BigWig |
| Software features | Data Visualisation, coverage analysis, File reformatting, normalization, GC plot analysis |
| Programming language(s) | Python |
| Licence | GPLv3 |
| Operating system(s) | Linux, Mac OS X |
| Contact: | deeptools@googlegroups.com |
Summary: User-friendly tools for the normalization and visualization of deep-sequencing data.
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Description
deepTools addresses the challenge of handling the large amounts of data that are now routinely generated from DNA sequencing centers. To do so, deepTools contains useful modules to process the mapped reads data to create coverage files in standard bedGraph and bigWig file formats. By doing so, deepTools allows the creation of normalized coverage files or the comparison between two files (for example, treatment and control). Finally, using such normalized and standardized files, multiple visualizations can be created to identify enrichments with functional annotations of the genome. For a gallery of images that can be produced, see http://f1000.com/posters/browse/summary/1094053
Links
- DeepTools Source code [ edit link ]
- DeepTools [ edit link ]
- DeepTools Binaries [ edit link ]
- DeepTools Mailing list [ edit link ]
References
To add a reference for DeepTools, enter the PubMed ID in the field below and click 'Add'.
Search for "DeepTools" in the SEQanswers forum / BioStar or:
| Web Search | Wiki Sites | Scientific |
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