MetaPhlAn version 3.1.0
I am looking to exclude certain species from my metaphlan output. I can’t find any details about the --ignore-markers argument. Can I do this in a level that is more specific than kingdom? For example, how can I exclude any one of these levels: o__Enterobacterales|f__Enterobacteriaceae|g__Cronobacter|s__Cronobacter_universalis
Thanks!
Hi @jxx419
The metaphlan markers are defined at the species level, so removing all the markers (markers info file here: http://cmprod1.cibio.unitn.it/biobakery3/metaphlan_databases/mpa_v29_CHOCOPhlAn_201901_marker_info.txt.bz2) from the species of interest will do the job
Hi, I am having similar issues. Not sure how to create a file to use with the --ignore_markers option. I have a list of species I would like to exclude since they appeared in my negative control sample. How do I prepare this input file for the parameter, please? Thanks!