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`