I am applying the posted tutorial of DADA2 + PacBio : Fecal Samples
but on sample data from PacBio website
So, what I did as follows:
(fastq sequences in HiFi folder)
path1 <- "~/Desktop/HiFi" # CHANGE ME to location of fastq files path.out <- "Figures/" path.rds <- "RDS/" fns1 <- list.files(path1, pattern="fastq.gz", full.names=TRUE) F27 <- "AGRGTTYGATYMTGGCTCAG" R1492 <- "RGYTACCTTGTTACGACTT" rc <- dada2:::rc theme_set(theme_bw())
#Remove Primers and Filter #Remove primers and orient reads: nops1 <- file.path(path1, "noprimers", basename(fns1)) prim1 <- removePrimers(fns1, nops1, primer.fwd=F27, primer.rev=dada2:::rc(R1492), orient=TRUE)
Then, I got this message:
No reads passed the primer detection.
So, I have a few questions:
1- I am wondering if these sequences are ccs reads to use in the analysis. The genomic facility will pass me demultiplexed sequences, so I need to start from ccs reads (dada2 R package).
2- May you please provide me with demo ccs sequences to work on and get more familiar with the analysis?
3- I’d like to confirm the files to use in Qiime2 that will be; dd2 (feature table), and st2 (representative sequences), correct? I believe these files are dataframe type, and I will need to convert them into qza, any help or suggestions?