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Repository deeptools_bam_coverage
Owner: bgruening
Synopsis: Wrapper for the deepTools: bamCoverage
deepTools address the challenge of visualizing the large amounts of data that
are now routinely generated from sequencing centers in a meaningful way. To do so,
deepTools contain useful routines to process the mapped reads data through removal of
duplicates and different filtering options to create coverage files in standard
bedGraph and bigWig file formats. deepTools allow 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 and a description of the tools see http://f1000.com/posters/browse/summary/1094053

https://github.com/deeptools/deepTools
doi: 10.1093/nar/gku365
Wikipage: https://github.com/deeptools/deepTools/wiki

Repository-Maintainer: Björn Grüning

https://github.com/deeptools/deepTools
Type: unrestricted
Revision: 19:3033c3fba046
This revision can be installed: True
Times cloned / installed: 4079
Dependencies of this repository

Repository data_manager_twobit_builder revision 9946bc39c834 owned by devteam

Contents of this repository

Name Description Version Minimum Galaxy Version
generates a coverage bigWig file from a given BAM or CRAM file 3.0.2.0 16.01

extension type mimetype subclass
deeptools_compute_matrix_archive galaxy.datatypes.binary:CompressedArchive True
deeptools_coverage_matrix galaxy.datatypes.binary:CompressedArchive True

Categories
ChIP-seq - Tools for analyzing and manipulating ChIP-seq data.
Convert Formats - Tools for converting data formats
Sequence Analysis - Tools for performing Protein and DNA/RNA analysis
Visualization - Tools for visualizing data