RDP LSU taxonomic training data formatted for DADA2 (trainingset 11)

<p>#Format RDP taxonomic training set for DADA2<br> #1  Wrangle the RDP trainingsets and unaligned data into the downloads folder by executing this from a terminal and move the file somewhere with &gt;30GB free<br> wget https://sourceforge.net/projects/rdp-classifier/files/RDP_Classifier_TrainingData/RDPClassifier_fungiLSU_trainsetNo11_rawtrainingdata.zip/download<br> wget http://rdp.cme.msu.edu/download/current_Fungi_unaligned.fa.gz<br> #2  Unzip the trainingset file and replace Us with Ts in the fasta by executing in terminal<br> awk 'NR%2==0 {gsub(/[uU]/,"T"); print} NR%2==1' /media/lauren/96BA-19E6/RDPClassifier_fungiLSU_trainsetNo11_rawtrainingdata/fungiLSU_train_012014.fa &gt; /media/lauren/96BA-19E6/RDPClassifier_fungiLSU_trainsetNo11_rawtrainingdata/fungiLSU_train_012014_lsu_fixed_v2.fa<br> #3  Summon the dada2 pkg<br> library(dada2);packageVersion("dada2")<br> #4  Transform the DADA2 formatted training fastas<br> path&lt;-"/media/lauren/96BA-19E6/RDPClassifier_fungiLSU_trainsetNo11_rawtrainingdata"<br> dada2:::makeTaxonomyFasta_RDP(file.path(path, "fungiLSU_train_012014_lsu_fixed_v2.fa"), file.path(path, "fungiLSU_taxid_012014.txt"),"/media/lauren/96BA-19E6/Upload/RDP_LSU_fixed_train_set_v2.fa",compress=FALSE)<br> dada2:::makeSpeciesFasta_RDP("/media/lauren/96BA-19E6/RDPClassifierLSU/current_Fungi_unaligned.fa", "/media/lauren/96BA-19E6/Upload/rdp_species_assignment_LSU_v2.fa", compress=FALSE)</p> <p>#5 Make the compressed DADA2 formatted training fastas in gz and zip format<br> dada2:::makeTaxonomyFasta_RDP("/media/lauren/96BA-19E6/RDPClassifier_fungiLSU_trainsetNo11_rawtrainingdata/fungiLSU_train_012014_lsu_fixed_v2.fa", file.path(path, "fungiLSU_taxid_012014.txt"),"/media/lauren/96BA-19E6/Upload/RDP_LSU_fixed_train_set_v2.fa.gz",compress=TRUE)<br> dada2:::makeTaxonomyFasta_RDP("/media/lauren/96BA-19E6/RDPClassifier_fungiLSU_trainsetNo11_rawtrainingdata/fungiLSU_train_012014_lsu_fixed_v2.fa", file.path(path, "fungiLSU_taxid_012014.txt"),"/media/lauren/96BA-19E6/Upload/RDP_LSU_fixed_train_set_v2.fa.zip",compress=TRUE)<br> dada2:::makeSpeciesFasta_RDP("/media/lauren/96BA-19E6/RDPClassifierLSU/current_Fungi_unaligned.fa", "/media/lauren/96BA-19E6/Upload/rdp_species_assignment_LSU_v2.fa.gz", compress=TRUE)<br> dada2:::makeSpeciesFasta_RDP("/media/lauren/96BA-19E6/RDPClassifierLSU/current_Fungi_unaligned.fa", "/media/lauren/96BA-19E6/Upload/rdp_species_assignment_LSU_v2.fa.zip", compress=TRUE)</p> <p> </p>