DADA2 compatibility ?

[emlas]

I wonder if R Studio (i.e.R 3.6.1.) is compatible with DADA2 package

[nirgrahamuk]

https://benjjneb.github.io/dada2/dada-installation.html

Install binaries from Bioconductor

Binary installation is available through the Bioconductor package repository. Binary installation of the current release version (1.14) requires R 3.6.1 and Bioconductor version 3.10:

if (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")
BiocManager::install("dada2", version = "3.10")

Allow installation of any additional packages requested. You are ready to start using DADA2!

[raytong]

Hi @emlas. Yes, I am using DADA2 package under R 3.6.1.

[emlas]

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"

[nirgrahamuk]

Did you forget to load the library?