Required Flags¶
These are the required flags that must be used during Execution. All of these commands must be used via the command line.
--runP / --runN [CMD]¶
- Specify a blastp or blastx annotation
- If - -runP is selected with a nucleotide input, frame selection will be ran and annotation stages will be executed with protein sequences (blastp)
- If - -runP is selected with a protein input, frame selection will not be ran and annotation will be executed with protein sequences (blastp)
- If - -runN is selected with nucleotide input, frame selection will not be ran and annotation will be executed with nucleotide sequences (blastx)
-i / --input [string] [CMD]¶
- Path to the transcriptome file (either nucleotide or protein)
-d / --database [multi-string] [CMD]¶
- Specify up to 5 DIAMOND indexed (.dmnd) databases to run similarity search against
--ini [string] [CMD]¶
- Point to entap_config.ini to specify file paths
- Default: entap_config.ini residing in the current working directory