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After qiime2 denoise my samples, some are gone

Hi, all!!

while I'm struggling to do beta diversity, I found that there is a problem on my table after denoise with DADA2. I double checked my manifest file and metadata file, I reassure that there are 9samples in total in both of them with exact information and file path. But after denoise-single, 3 of them are gone. Only 6 samples remain in table after dada2 denoise and 3 are gone. Below is my code for denoise.

qiime dada2 denoise-single --i-demultiplexed-seqs demux.qza --p-trim-left 0 --p-trunc-len 550 --o-representative-sequences rep-seqs-dada2.qza --o-table table-dada2.qza --o-denoising-stats stats-dada2.qza --verbose

I need help :( thank you

qiime2 denoise sample
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written by pple2202 • pple2202

Plus:

I also tried denoise with deblur, it shows only 2 samples, 7 samples are gone. I totally have no idea what is wrong :(

Below is deblur code I input.

qiime quality-filter q-score --i-demux demux.qza --o-filtered-sequences demux-filtered.qza --o-filter-stats demux-filter-stats.qza qiime deblur denoise-16S --i-demux.qza --p-trim-length 550 --o-representative-sequences rep-seqs-deblur.qza --o-table table-deblur.qza --p-sample-stats --o-stats deblur-stats.qza

Please HELP

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written by pple2202 • pple2202

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