We want to obtain the OTU (ASV) table from fastq, but the results of two people using the same qiime2 parameters are different: one person has more than 5,000 ASV, and the other has more than 3,000 ASV.
Parameter:
SILVA_132_QIIME_release
Raw sequencing data were analysed by QIIME2. In brief, the data were imported into QIIME2 and demultiplexed, a DADA2 pipeline was used for sequencing quality control, and a feature table was constructed with the following options: qiime dada2 denoise-paired—i-demultiplexed-seqs demux.qza—p-trim-left-f 0—p-trim-left-r 0—p-trunc-len-f 248 —p-trunc-len-r 200 —o-table table—o-representative-sequences rep-seqs.
Thank for your attention!
Hi! Is the version of Qiime 2 also the same?
No. He has gone for another lab. I think the qiime2 version is different.
However, different qiime2 version should not produce so much difference. Right？ 
Hi @Wang_cs001632 - we need more information in order to effectively help you:
- Please provide the version of QIIME 2 used
- Please list all relevant commands run (copy and paste please)
- Please provide detailed information about what you think is the error you are seeing.
If possible, please upload QZVs (so that we can view data provenance).
1 Like
Thank for your reply.trimzch.qzv (299.7 KB)
This is my qzv. I don't have his qzv. My version is qiime2 2019.7.
Might you can infer the reason of different through your experience?
You have only provided one result - there is nothing to compare it to to ascertain a difference.
Sorry, his version is lost. Could you provide a few possible reason? Before this qzv, my result is same with his. However, we different after qiime dada2 denoise-paired—i-demultiplexed-seqs demux.qza—p-trim-left-f 0—p-trim-left-r 0—p-trunc-len-f 248 —p-trunc-len-r 200 —o-table table—o-representative-sequences rep-seqs
- Changing the trunc or trim parameters, even by 1 nt, will produce entirely new ASVs
- Different versions of DADA2/q2-dada2
Without the provenance for both datasets its not possible for us to say anything more specific.
Hope that helps!
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