Nicholas_Bokulich,I have the same problem with her. I have 24 samples, but after denoising there are 18 sample left. It seems that the missing samples are all zero non-chimeric, the image as follows:
In the process of denoising, I reserved the area with good quality to the maximun according to demux result, which is shown in the follow:qiime dada2 denoise-paired --i-demultiplexed-seqs test-24.qza --p-trunc-len-f 299 --p-trunc-len-r 276 --output-dir result
ps:the qiime version 2019.1,I have 301 nts sequences
I don't quite understand what you mean. I'd like to repeat the problem in its entirety.
First, I input my sample sequences(24 sample/48 sequences), creat and enter the absolute working path at the same time. Then the data format was been standardized. After that the step of "qiime demux summarize" was run trouble-free. The 24 samples‘ result was shown as follows:
Based on the results above, I decided to use the following codes to denoise:
time qiime dada2 denoise-paired \
--i-demultiplexed-seqs cecum.qza \
--p-trunc-len-f 299 \
--p-trunc-len-r 280 \
To my confusion, 6 samples were missing from the pair-end denoise results.