Just hoping to get some advice on using dada2 for PacBio CSS data! This is the first time I have worked with PacBio CSS, my intention is to use the Qiime2 pipeline, however I read on here that the version dada2 within qiime2 does not yet support long-read data. Thus, I am using this guide (DADA2 + PacBio: Fecal Samples) to process the data in R.
I am getting an error message when trying to run the removePrimers command, this is the latest code I have attempted based on the guidance here (removePrimers: Removes primers and orients reads in a consistent direction. in dada2: Accurate, high-resolution sample inference from amplicon sequencing data)
F1 <- "~Documents/16SCSS Jun21/R Dada2/F1-CSS.fastq"
f1n <- file.path(F1, "F1-CCS.fastq")
path.out <- "Figures/"
path.rds <- "RDS/"
F27 <- "AGAGTTTGATCMTGGCTCAG"
R1492 <- "TACGGYTACCTTGTTAGGACTT"
rc <- dada2:::rc
primF1 <- removePrimers(f1n, path.out, primer.fwd = F27, primer.rev = R1492, trim.fwd = TRUE, trim.rev = TRUE, orient = TRUE, verbose = TRUE)
When I try to run this I get the following error message-
Error in removePrimers(f1n, path.out, primer.fwd = F27, primer.rev = R1492, :
Some input files do not exist.
Not really sure what to make of this, I have defined the path to the fastq file, does anyone know where I should start with troubleshooting this?
Thank you for any advice you can give!