I am using QIIME2 v. 2018.8 and I am denoising my paired end read data with DADA2. I am seeing a discrepancy between the number of samples in the denoised-stats file (78, the number that should be there), and the number of samples in the feature table (73, missing 5 samples). Here is the command I ran to produce the files:
qiime dada2 denoise-paired --i-demultiplexed-seqs demux-seqs.qza --p-trunc-len-f 251 --p-trunc-len-r 218 --p-n-threads 15 --o-representative-sequences rep-seqs.qza --o-table table.qza --o-denoising-stats denoising-stats --verbose
I know the sequences aren't the best, with a lot that have low sequence counts/non-chimeric output. I thought it might be removing samples with low merged/non-chimeric sequences, but looking at the denoise stats I have 18 that have zero non-chimeric sequences and only 5 are missing. If you could help me determine why it's removing samples/why those 5 specifically I would really appreciate it.
The 5 missing samples are: ES1-1-B_10-10-17_8, ES1-1-B_12-08-17_67, ES1-1-D_04-06-18_186, ES1-3-A_09-29-17_-3, ES1-3-D_02-02-18_123
Here's the command I ran to visualize the stats file and the table:
qiime metadata tabulate --m-input-file denoising-stats.qza --o-visualization vis-denoising-stats.qzv
qiime feature-table summarize --i-table table.qza --o-visualization vis-table.qzv --m-sample-metadata-file MappingFILE_Round2_20180814.txt
I'm also attaching the files if they're helpful.
table.qza (25.2 KB)
denoising-stats.qza (12.8 KB)
rep-seqs.qza (25.2 KB)
vis-table.qzv (327.5 KB)
vis-denoising-stats.qzv (1.2 MB)