Just hoping to get some advice, after running our 16S amplicon sequencing data through dada2 it seems to be concluding >80% of the reads are chimeras, leaving us with too few reads to make any robust observations. We were already suspicious the data might have some chimera problems… but I would like to be confident that there are in fact this proportion of chimeras before I conclude it is a bust… any advice? See below for the code & demux.qzv file. I am running this on qiime2-2018.2.
qiime dada2 denoise-paired --i-demultiplexed-seqs demux.qza --o-table table --o-representative-sequences rep-seqs --p-trim-left-f 20 --p-trim-left-r 20 --p-trunc-len-f 120 --p-trunc-len-r 135 --p-chimera-method consensus --verbose
demux (1).qzv (290.2 KB)