Basic Usage Flags¶
These are just some basic/common flags to use during Execution. You’ll see these repeated on the other pages. All these flags can only 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 configured databases you would like to search agianst
--out-dir [string] [CMD]¶
- Specify an output directory for all of the files generated by EnTAP
- Default: Current working directory
-t / --threads [integer] [CMD]¶
- Specify thread count for execution
--ini [string] [CMD]¶
- Point to entap_config.ini to specify file paths
- Default: entap_config.ini residing in the current working directory
--version [CMD]¶
- Prints the current EnTAP version you are running
-a / --align [string] [CMD]¶
- Path to alignment file (either SAM or BAM format)
- Note: Ignoring this flag will skip expression filtering
- If you have ran alignment with single end reads be sure to use the - -single-end flag as well (paired-end is default)
- Be sure to specify an FPKM threshold