diff --git a/PhyloToL-Part-1:-GF-assignment.md b/PhyloToL-Part-1:-GF-assignment.md index 10ef24c..608995b 100644 --- a/PhyloToL-Part-1:-GF-assignment.md +++ b/PhyloToL-Part-1:-GF-assignment.md @@ -94,7 +94,7 @@ Available parameters are: #### 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: +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`