In brendanf/tzara: Cluster long amplicons using dada2 denoising on variable regions

knitr::opts_chunk$set(
  collapse = TRUE,
  comment = "#>"
)

library(tzara)
library(inferrnal)
library(LSUx)
library(ShortRead)

The sample sequences are the 37S pre-rDNA (including SSU, ITS1, 5.8S, ITS2, LSU) from eleven Saccharomyces genomes.

rDNA37 <- readFasta(system.file(file.path("extdata", "RDN37.fasta"), package = "tzara"))

Find the 32S region

pos <- lsux(rDNA37)

Choose the region from 5.8S to LSU5 (prior to the beginning of D5).

extract_region(rDNA37, positions = pos, "5_8S", "LSU5")

brendanf/tzara documentation built on March 11, 2021, 5:40 a.m.