RE: Samples missing from DADA2 table but not denosing stats

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

1 Like

Yikes, not sure I have any help to offer, but does this mean that all sequences failed due to quality? @benjjneb

Out of curiosity, could you post your quality scores? Ben

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 \
--output-dir result
To my confusion, 6 samples were missing from the pair-end denoise results.

Are there any mistakes in my previous steps? Did I pick the wrong criteria?
I really need those samples. Can you give me a hand?

1 Like

No, I don’t think you did anything wrong.

all 24 samples were demuxed with adequate sequencing depth.

all 24 samples lose all sequences after filtering step in DADA2/denoise.

It’s just strange to see you lose all of the sequences. Ben

1 Like

I think these values are too high. Try truncating more, maybe 290 + 260 (or shorter if you can afford it)

Good luck!

1 Like

Agreed with Nicholas

  • forward I would truncate @ 240-260
  • reverse I would truncate @ 160-180

This topic was automatically closed 31 days after the last reply. New replies are no longer allowed.