From 158d1d4aefab00c1f5d672aa5c5a603052ab584c Mon Sep 17 00:00:00 2001 From: Godwin Ani Date: Tue, 13 Aug 2024 10:29:13 -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 b45adee..4f9b2a2 100644 --- a/PhyloToL-Part-1:-GF-assignment.md +++ b/PhyloToL-Part-1:-GF-assignment.md @@ -93,7 +93,7 @@ Available parameters are: | --seq_count |int|-| minimum number of sequences after assigning OGs | -####Index Switching (Cross plate contamination) +#### Index Switching (Cross plate contamination) As you run PhyloToL part 1 on transcriptomes, you might want to remove sequences from your assembled transcripts that are a result of index switching. This is done by (LAK and ACL on XPC removal process with conspecific file). To include this parameter to your PhyloToL part 1 run, you will need to add the '--xplate_contam --conspecific_names Conspecific.txt' flag to the command line as follow: `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`