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 - #17 by ebolyen) was due to have fake quality scores.
How would you suggest going about fixing this?