Galaxy |

Repository revision

Repository bam_to_scidx

Name: bam_to_scidx

Owner: iuc

Synopsis: Contains a tool that converts a BAM file to an ScIdx file.

Detailed description:

Converts BAM data to ScIdx, the Strand-specific coordinate count format, which is used by tools within
the Chip-exo Galaxy flavor.  ScIdx files are 1-based.  The format consists of 5 columns: the chromosome,
the position of the genomic coordinate, the number of tags on the forward strand, the number of tags on
the reverse strand and the number of total tags on the position.  With pair-end reads, only the 5’ end of
READ1 will be used to create the ScIdx data file.  Tools that use this format include GeneTrack and MultiGPS.

Content homepage: https://github.com/seqcode/cegr-tools/tree/master/src/org/seqcode/cegrtools/bamtoscidx

Development repository: https://github.com/galaxyproject/tools-iuc/tree/master/tools/bam_to_scidx

Link to this repository revision: https://toolshed.g2.bx.psu.edu/view/iuc/bam_to_scidx/11fc60f0e942

Clone this repository: hg clone https://toolshed.g2.bx.psu.edu/repos/iuc/bam_to_scidx

Type: unrestricted

Revision: 3:11fc60f0e942

This revision can be installed: True

Times cloned / installed: 724