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GenesToBed tool help

GenesToBed (2019_07-8-g5a9c094)

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'.

GenesToBed changelog

GenesToBed 2019_07-8-g5a9c094

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

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