From 530594b2b1beb6ecfcacf4a06e1f4956bf06eb2c Mon Sep 17 00:00:00 2001 From: Godwin Ani Date: Mon, 12 Aug 2024 16:16:04 -0400 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 7d564c6..273242f 100644 --- a/PhyloToL-Part-1:-GF-assignment.md +++ b/PhyloToL-Part-1:-GF-assignment.md @@ -92,7 +92,7 @@ Available parameters are: | --maxlen |int|-| Maximum transcript length | | --seq_count |int|-| minimum number of sequences after assigning OGs | -#### To run the PhyloToL part 1 for both processing transcriptomes and removing sequences that resulted from index switching (cross plate contamination), run: +#### To run the PhyloToL part 1 for both processing transcriptomes and removing sequences that resulted from index switching (cross plate contamination), run (LAk and ACL): `python Scripts/wrapper.py --first_script 1 --last_script 7 --assembled_transcripts AssembledTranscripts --output . --genetic_code Gcode.txt --databases Databases --xplate_contam --conspecific_names Conspecific.txt > log.txt`