high chimera rate in dada2

[Nicholas_Bokulich]

Hi @Claire010,
90% is indeed high! You should check out these related forum topics for more discussion on how to troubleshoot and adjust:

Dada2 filtering out >80% of reads as chimeras!

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. Code- q…

loss of reads after DADA2 as chimeras

Hi @Shruthi, 70% is indeed quite a bit, hopefully we can improve on that a bit. Here are some things to consider and follow up questions: Your trim/truncating parameters look good to me, with plenty of overlap for merging etc. however, DADA2 can struggle a bit with chimera detection if non-biological sequences are left in your reads, for example if you haven't removed your adapters, barcodes, primers etc. So this is a good starting point to make sure you only have biological sequences in your…

low proportion of non-chimeric reads

Dear all I'm puzzled by the low proportion of non-chimeric reads I obtain with the command: qiime dada2 denoise-paired --i-demultiplexed-seqs demux-paired-end.qza --p-trim-left-f 0 --p-trim-left-r 0 --p-trunc-len-f 280 --p-trunc-len-r 220 --o-representative-sequences rep-seqs-dada2.qza --o-table table-dada2.qza --output-dir denoising --p-n-threads 48 denoising_stats.qzv: sample-id input filtered denoised merged non-chimeric #q2:types numeric numeric numeric numeric n…

Good luck!