# high chimera rate in dada2 **URL:** https://forum.qiime2.org/t/high-chimera-rate-in-dada2/16935 **Category:** User Support **Tags:** chimera, dada2 **Created:** [October 6, 2020, 5:36pm UTC](https://forum.qiime2.org/t/high-chimera-rate-in-dada2/16935 "2020-10-06T17:36:41Z") **Posts on this page:** 1 **Showing post:** 2
### Author: ![Nicholas\_Bokulich](https://forum.qiime2.org/user_avatar/forum.qiime2.org/nicholas_bokulich/32/19937_2.png) [@Nicholas\_Bokulich](https://forum.qiime2.org/u/Nicholas_Bokulich) #### Post date: [October 14, 2020, 8:25am UTC](https://forum.qiime2.org/t/high-chimera-rate-in-dada2/16935/2 "2020-10-14T08:25:43Z")
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!](https://forum.qiime2.org/t/dada2-filtering-out-80-of-reads-as-chimeras/7866): > > 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](https://forum.qiime2.org/t/loss-of-reads-after-dada2-as-chimeras/9503/2): > > 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](https://forum.qiime2.org/t/low-proportion-of-non-chimeric-reads/12497): > > 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! --- _[View the full topic](https://forum.qiime2.org/t/high-chimera-rate-in-dada2/16935)._