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Repository bam_to_bigwig
Name: bam_to_bigwig
Owner: brad-chapman
Synopsis: Generate BigWig coverage files from BAM files. Allows gapped reads to be split (useful for RNA-Seq).
Create a BigWig file of coverage data from a BAM file using BEDtools with a bedgraph intermediate. Produces BigWig files suitable for display at UCSC. Requires pysam, BEDtools and bedGraphToBigWig.
Content homepage: https://github.com/lparsons/galaxy_tools/tree/master/tools/bam_to_bigwig
Development repository: https://github.com/lparsons/galaxy_tools/tree/master/tools/bam_to_bigwig
Link to this repository: https://toolshed.g2.bx.psu.edu/view/brad-chapman/bam_to_bigwig/9163e1db4c16
Clone this repository: hg clone https://toolshed.g2.bx.psu.edu/repos/brad-chapman/bam_to_bigwig
Type: unrestricted
Revision: 6:9163e1db4c16
This revision can be installed: True
Times cloned / installed: 1300
Dependencies of this repository

Repository dependencies - installation of these additional repositories is required
Repository package_python_2_7_10 revision bd7165ea6526 owned by iuc (prior install required)
Repository package_zlib_1_2_8 revision 411985b46ae8 owned by iuc (prior install required)
Repository package_readline_6_3 revision ca1a9400d4e1 owned by iuc (prior install required)
Repository package_bzlib_1_0 revision af4887e1f595 owned by iuc (prior install required)
Repository package_xz_5_0_5 revision 944f93d45594 owned by iuc (prior install required)
Repository package_sqlite_3_8_3 revision c8a5c11cc921 owned by iuc (prior install required)
Repository package_gdbm_1_11 revision ed2537bccffc owned by iuc (prior install required)
Repository package_ncurses_6_0 revision 0efde9889efd owned by iuc (prior install required)
Repository package_ncurses_6_0 revision 0efde9889efd owned by iuc (prior install required)
Repository package_libtool_2_4 revision 7f67694b167c owned by iuc (prior install required)
Repository package_bedtools_2_24 revision 3416a1d4a582 owned by iuc
Repository package_ucsc_tools_312 revision 2d6bafd63401 owned by iuc

Tool dependencies - repository tools require handling of these dependencies
Name Version Type
bedtools 2.24 package
pysam 0.8.3 package
ucsc_tools 312 package

Contents of this repository

Valid tools - click the name to preview the tool and use the pop-up menu to inspect all metadata
Name Description Version Minimum Galaxy Version
Calculates coverage from a BAM alignment file 0.2.0 any

Categories
Convert Formats - Tools for converting data formats
SAM - Tools for manipulating alignments in the SAM format
Visualization - Tools for visualizing data

Rating
2