Question: QIIME2 Clustering and DeNoising
gravatar for rahul.yadav
9 months ago by
rahul.yadav10 wrote:

Hello I am stuck with the denoising and clustering step in QIIME2. When I am setting --p-trunc-len as “0” (ZERO), I am getting a varying length of rep-seq set and the otus as well. The outputs of the denoising step that are needed in the clustering step do not work for --p-trunc-len 0 (the output file of denoise at trunc len 0 ) for clustering but work for --p-trunc-len 200 or any value other than 0. I also read the DADA2 Paper, where they say that the tool need same length of sequences in order to denoise. Failing to have that the tool itself fails in denoising. And when denoising at --p-trunc-len 0, I am getting the representative sequences of varying length, which i feel is not denoising in this case.

I also tried to analyse by keeping the --p-trunc-len at 0 (ZERO) and --p-trunc-q at 20. But i am not able to proceed with further steps. However when I keep the --p-trunc-len anything other than 0(ZERO) and --p-trunc-q at 20 clustering works.

Please explain the reason behind this and how should i proceed for analysis and also deal with this kinds of errors.

Thanking You in advance.

Best Regards, Rahul

ADD COMMENTlink modified 7 months ago by Biostar ♦♦ 20 • written 9 months ago by rahul.yadav10
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