# Denoising vs OTU picking methods **URL:** https://forum.qiime2.org/t/denoising-vs-otu-picking-methods/5360 **Category:** User Support **Tags:** dada2, asv, otus **Created:** [August 1, 2018, 4:35pm UTC](https://forum.qiime2.org/t/denoising-vs-otu-picking-methods/5360 "2018-08-01T16:35:07Z") **Posts on this page:** 1 **Showing post:** 5
### Author: ![Dchung](https://forum.qiime2.org/letter_avatar_proxy/v4/letter/d/eb8c5e/32.png) [@Dchung](https://forum.qiime2.org/u/Dchung) #### Post date: [August 2, 2018, 1:33pm UTC](https://forum.qiime2.org/t/denoising-vs-otu-picking-methods/5360/5 "2018-08-02T13:33:16Z")
Thank you for the reply, That makes more sense. I may have used the wrong parameters. > [@Mehrbod\_Estaki](#): > > Could you provide us with the full commands you used to run dada2 please. My guess is that without adequate truncating values sets you will have dropped most of your reads before even reaching the actual denoising step. DADA2 denoise step is as below: > qiime dada2 denoise-paired > --i-demultiplexed-seqs $JOB\_DIR/demux.qza > --o-table $JOB\_DIR/table.qza > --o-representative-sequences $JOB\_DIR/rep-seqs.qza > --o-denoising-stats $JOB\_DIR/denoising-stats.qza > --p-trim-left-f 0 > --p-trim-left-r 0 > --p-trunc-len-f 0 > --p-trunc-len-r 0 > --p-n-threads 5 I didn't truncate any sequences because I thought the quality wasn't good and I might loose too many seqs. I went back to my qiime1 steps and found that I used the default parameters on _split\_libraries\_fastq.py_ step, which had "-q" (--phred\_quality\_threshold The maximum unacceptable Phred quality score) as 3. The open reference otu picking with this data gave me ridiculously high numbers of OTUs(80000s) with singletons and chimeras removed. I'm thinking the parameter _-q 3_ could've been too lenient compared to qiime2 filters. Please let me know if I should change the parameters. Cheers, --- _[View the full topic](https://forum.qiime2.org/t/denoising-vs-otu-picking-methods/5360)._