So I am running some samples using Pacbio amplicon sequencing. Due to its method of generatinga consensus sequence from many sequences, my quality scores are extremely high.
Thus becomes an issue when I attempt to run DAD2. It presents the following error
Error in dada(drps[1:i], err = NULL, selfConsist = TRUE, multithread = multithread, :
derep$quals matrix has an invalid maximum Phred Quality Scores of 93
I thought I could get around this by just giving all of my sequences a generic quality score, however, then I got the following error:
Error in err[c(1, 6, 11, 16), ] <- 1 :
incorrect number of subscripts on matrix
Which according to another post (Doing taxonomy analysis and getting abundancies with manifests) was due to have fake quality scores.
How would you suggest going about fixing this?