From c8c42a1e89a97a612fc8296a1fc6e42c0f0d2221 Mon Sep 17 00:00:00 2001 From: Godwin Ani Date: Mon, 12 Aug 2024 13:08:28 -0400 Subject: [PATCH] Updated PhyloToL Part 1: GF assignment (markdown) --- PhyloToL-Part-1:-GF-assignment.md | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/PhyloToL-Part-1:-GF-assignment.md b/PhyloToL-Part-1:-GF-assignment.md index 96599ed..1a6d523 100644 --- a/PhyloToL-Part-1:-GF-assignment.md +++ b/PhyloToL-Part-1:-GF-assignment.md @@ -71,8 +71,8 @@ Replacing the PhyloToL Hook DB with a user-defined set of gene families is strai Role of each script -* **Main inputs** : A folder containing the assembled transcripts, a folder containing the Databases, and a folder containing the scripts. -* **Outputs** : ReadyToGo files (AA and NTD), taxon summary, and sequence summary. +* **Main inputs** : A folder containing the assembled transcripts, a folder containing the Databases, and a folder containing the [Scripts](https://github.com/Katzlab/PhyloToL-6/tree/main/PTL1/Transcriptomes/Scripts). +* **Outputs** : ReadyToGo files (AA and NTD) and taxon summary. * *Optional inputs : Gcodes.txt and Conspecific.txt * *The Gcodes.txt is a tab separated txt file containing the genetic code of the taxa. This will most likely not be needed except for some organisms like ciliates. * _Example:_ @@ -102,7 +102,7 @@ To process transcriptomes, run: * --output = path to output folder * --genetic_code = specified genetic code, name of .txt file with Genetic codes * -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 ### Processing genomes