https://github.com/pjdiebold/OIL-PCR_Linking_plasmid-based_beta-lactamases
Tip revision: 6d5b25dfa6d67703f06f74c24f7efe27bcf9d8dd authored by pjdiebold on 15 June 2021, 20:27:54 UTC
Update README.md
Update README.md
Tip revision: 6d5b25d
MOTHUR_classify_filtered.sh
#!/bin/bash
WRK=/workdir/users/pd378/oilPCR/bulk_process_all_OIL_for_paper #UPDATE THE WORKDIR
FASTAS_ALL=$WRK/s6_cluster_otu/filtered_uniqs/uniq_clustered_otus.fa
SILVA=/workdir/users/pd378/DataBases/MOTHUR_SILVA/silva.nr_v132.V4_oil
cd $FASTAS
/programs/mothur/mothur "#classify.seqs(fasta=$FASTAS_ALL, template=$SILVA.align, taxonomy=$SILVA.tax, pro
#/programs/mothur/mothur "#classify.seqs(fasta=ALL_OTUs.fasta, template=$SILVA/silva.nr_v132.align, taxonomy=$SILVA/silva.nr_v132.tax, processors=20)"
