diff --git a/QuickStart-EukPhylo.md b/QuickStart-EukPhylo.md index c5b1cc7..e309771 100644 --- a/QuickStart-EukPhylo.md +++ b/QuickStart-EukPhylo.md @@ -60,7 +60,8 @@ Code parameters: |`-o` | Path to output folder.| |`--genetic_code` | Specified genetic code, name of .txt file with Genetic codes; optional.| |`-d` | Path to Databases folder.| -|`> log.txt` | If added to the end of the command, it will output a log file with progress, warning, or error messages.| +|`> log.txt` | If added to the end of the command, it will output a log file with progress, warning, or error messages.| +|`-x`| Run cross-plate contamination (XPC). Only available for transcriptomes.| ### Output: 1. **ReadyToGo files = AA, NTD** @@ -70,8 +71,6 @@ Code parameters: EukPhylo part 1 for transcriptomes is composed of 7 scripts. User can choose to start or stop at each step by changing the -1 and/or -2 options. If a user chooses to use their own gene family database, they need to replace the Hook.fasta file in the Databases folder and build a diamond version of their own file; with adjusting the naming system of sequences as the only requirement. -To add the XPC option, only available for transcriptomes, user need to add the -x option in their command line. - ## Genomes: ### Set Up: * A folder called “CDS” with your CDS fasta files