TranscriptsToBed.md

TranscriptsToBed tool help

TranscriptsToBed (2024_08-113-g94a3b440)

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

Mandatory parameters:
  -mode <enum>      Mode: gene = start/end of the transcript, exon = start/end of all exons of the transcript.
                    Valid: 'gene,exon'

Optional parameters:
  -in <file>        Input TXT file with one transcript name per line. If unset, reads from STDIN.
                    Default value: ''
  -out <file>       Output BED file. If unset, writes to STDOUT.
                    Default value: ''
  -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).

TranscriptsToBed changelog

TranscriptsToBed 2024_08-113-g94a3b440

2023-05-25 First version.

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