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

<p>I used a machine with Ubuntu 16.04 and DADA2 (vsn 1.5.2) to coax the Ribosomal Database Project's Training set 11 and the current release of the RDP database (for the unaligned fasta) into a DADA2 compatible format. If you use this, please cite the original sources too!</p> <p><br> #1 Wrangle the RDP trainingsets and unaligned data into the downloads folder either by manually downloading them or by executing this from a terminal and move the file somewhere with <30GB free</p> <p>I used wget in a terminal:<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</p> <p>#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/fungallsu/RDPClassifier_fungiLSU_trainsetNo11_rawtrainingdata/fungiLSU_train_012014.fa > /media/lauren/96BA-19E6/fungallsu/RDPClassifier_fungiLSU_trainsetNo11_rawtrainingdata/fungiLSU_train_012014_lsu_fixed.fa</p> <p>#3 In R.Studio, summon the dada2 pkg <br> library(dada2);packageVersion("dada2")</p> <p>#4 Transform the RDP formatted training fastas<br> path<-"~"#change this to where your files sit on your computer<br> dada2:::makeTaxonomyFasta_RDP(file.path(path, "fungiLSU_train_012014_lsu_fixed.fa"), file.path(path, "fungiLSU_taxid_012014.txt"),"fungiLSU_trainset_012014.fa.gz")<br> dada2:::makeSpeciesFasta_RDP("current_Fungi_unaligned.fa", "rdp_species_assignment_LSU.fa")