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