I have been trying to run my Illumina Miseq data based on DADA2 pipeline tutorial (1.12 below). I am stuck on plotQualityProfile
What did I do wrong......
path <- "~/RSH2265/DATA2" # CHANGE ME to the directory containing the fastq files after unzipping.
list.files(path)
[1] "SH-2265-RhizoStr1_S1_L001_R1_001.fastq" "SH-2265-RhizoStr1_S1_L001_R2_001.fastq"
[3] "SH-2265-RhizoStr2_S2_L001_R1_001.fastq" "SH-2265-RhizoStr2_S2_L001_R2_001.fastq"
fnFs <- sort(list.files(path, pattern="_R1_001.fastq", full.names = TRUE))
fnRs <- sort(list.files(path, pattern="_R2_001.fastq", full.names = TRUE))
Extract sample names, assuming filenames have format: SAMPLENAME_XXX.fastq
sample.names <- sapply(strsplit(basename(fnFs), "_"), [, 1)
plotQualityProfile(fnFs[1:2])
Error in plotQualityProfile(fnFs[1:2]) :
could not find function "plotQualityProfile"