Chloroplast Taxonomy Assignment.Rmd

---
title: "R Notebook"
output: html_notebook
---


```{r}
#0.1 Set working directory
setwd("~/Dropbox/UTS/PhD/Projects/Chapter1_Vibrio_latitude_study/Data/16S/Data")

library(dada2)
library(tidyverse)
kptSilva138dfPlastid <-read_csv('Chloroplast.csv')
kptSilva138df = subset(kptSilva138dfPlastid, select = c(ASV))
kptSilva138df <- distinct(kptSilva138df)

kpPlastid <- assignTaxonomy(seqs=kptSilva138df$ASV, refFasta = 'pr2_version_4.12.0_16S_dada2.fasta',  tryRC = T, outputBootstraps = T, minBoot = 50, multithread = T)
kpPlastiddf<-as.data.frame(kpPlastid)
kpPlastiddf$asv<-rownames(kpPlastiddf)
write_csv(kpPlastiddf,'PR2tax.csv')
```