From 2b35b2edcc127f1dec99dd9bf1baaa31dee265aa Mon Sep 17 00:00:00 2001 From: Auden Cote-L'Heureux <52716489+AudenCote@users.noreply.github.com> Date: Fri, 10 Jan 2025 10:54:10 -0500 Subject: [PATCH] Updated PhyloToL Part 1: GF assignment (markdown) --- PhyloToL-Part-1:-GF-assignment.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/PhyloToL-Part-1:-GF-assignment.md b/PhyloToL-Part-1:-GF-assignment.md index d29fd75..193d572 100644 --- a/PhyloToL-Part-1:-GF-assignment.md +++ b/PhyloToL-Part-1:-GF-assignment.md @@ -103,7 +103,7 @@ Other available parameters are: | --assembled_transcripts |string|Path to a folder of assembled transcripts, assembled by rnaSPAdes. | Each assembled transcript file name should start with a unique 10 digit code, and end in "_assembledTranscripts.fasta", E.g. Op_me_hsap_assembledTranscripts.fasta | | --databases| string| Path to databases folder | The folder should contain all 3 databases| | --output|string|Path for the output files | An "Output" folder will be created at this directory to contain all output files. By default this folder will be created at the parent directory of the Scripts folder | -|--xplate_contam |flag (true/false) | include or exclude | Run cross-plate contamination removal (includes all files) | +|--xplate_contam |flag (true/false) | include or exclude the argument | Run cross-plate contamination removal (includes all files) | | --genetic_code |string|A .txt or .tsv with two tab-separated columns, the first with the ten-digit codes and the second column with the corresponding genetics codes| If all of your taxa use the same genetic code, you may enter it here. Alternatively, if you need to use a variety of genetic codes but know which codes to use, you may fill give here the path to a file. | |--conspecific_names |string| A .txt or .tsv file with two tab-separated columns; the first should have 10 digit codes, the second species or other identifying names|This is used to determine which sequences to remove (only between "species") in index switching (cross-plate contamination) assessment. | | --minlen |integer| any positive integer| Minimum transcript length |