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GenesToBed.md

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GenesToBed tool help

GenesToBed (2024_08-113-g94a3b440)

Converts a text file with gene names to a BED file.

Mandatory parameters:
  -source <enum>    Transcript source database.
                    Valid: 'ccds,ensembl'
  -mode <enum>      Mode: gene = start/end of all transcripts, exon = start/end of all exons of all transcripts.
                    Valid: 'gene,exon'

Optional parameters:
  -in <file>        Input TXT file with one gene symbol per line. If unset, reads from STDIN.
                    Default value: ''
  -out <file>       Output BED file. If unset, writes to STDOUT.
                    Default value: ''
  -fallback         Allow fallback to all source databases, if no transcript for a gene is defined in the selected source database.
                    Default value: 'false'
  -anno             Annotate transcript identifier in addition to gene name.
                    Default value: 'false'
  -test             Uses the test database instead of on the production database.
                    Default value: 'false'

Special parameters:
  --help            Shows this help and exits.
  --version         Prints version and exits.
  --changelog       Prints changeloge and exits.
  --tdx             Writes a Tool Definition Xml file. The file name is the application name with the suffix '.tdx'.
  --settings [file] Settings override file (no other settings files are used).

GenesToBed changelog

GenesToBed 2024_08-113-g94a3b440

2017-02-09 Added option to annotate transcript names.

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