Frame Selection Flags¶
These are the flags specific to Frame Selection using either GeneMarkS-T or TransDecoder. These will be used via the command line (denoted CMD) or ini file (denoted INI).
General Flags¶
--frame-selection [integer] [INI]¶
- Specify the frame selection software to use
- GeneMarkS-T
- TransDecoder (default)
--complete [INI]¶
- Tell EnTAP to mark all of the transcripts as ‘complete’. This will only be seen in the final output and will not affect the run.
TransDecoder Specific Flags¶
--transdecoder-m [INI]¶
- Specify the minimum protein length
--transdecoder-no-refine-starts [INI]¶
- Specify this flag if you would like to pipe the command, ‘–no_refine_starts’ to TransDecoder.
- “This will ‘start refinement identifies potential start codons for 5’ partial ORFs using a PWM, process on by default”. (From TransDecoder documentation)
- Default: False