Deblur stats question

Hi all,

I have a question about the columns in the deblur stats artefact generated by the --o-stats flag when running qiime deblur denoise-16S.
A few of my samples have very low numbers of input reads (likely a failed PCR or poor quality input). When I look at the deblur stats they are 0 in every column after reads-raw. I assume this is because there are no non-singleton reads in my samples so everything is removed in the first step. Is this correct? If not, can somebody please explain what is happening.

I have included the relevant samples from the output and command used below for reference (the input demux-filtered.qza is the output from qiime quality-filter q-score).
All the best,

sample-id reads-raw unique-reads-derep reads-derep unique-reads-deblur reads-deblur unique-reads-hit-artifact reads-hit-artifact unique-reads-chimeric reads-chimeric unique-reads-hit-reference reads-hit-reference unique-reads-missed-reference reads-missed-reference
SampleA 42 0 0 0 0 0 0 0 0 0 0 0 0
SampleB 16 0 0 0 0 0 0 0 0 0 0 0 0
qiime deblur denoise-16S \
                --i-demultiplexed-seqs demux-filtered.qza \
                --p-trim-length 150 \
                --p-sample-stats \
                --p-jobs-to-start 8 \
                --p-no-hashed-feature-ids \
                --o-table feature-table.qza \
                --o-representative-sequences rep-seqs.qza \
                --o-stats deblur-stats.qza

Hi @cazzlewazzle89,

Welcome back to the :qiime2: forum!

The issue is actually what you mentioned initially, that these samples have very low numbers of input (i.e. raw) reads. There are no parameters that you can modify on your end to retain read counts this low. If this is only an issue for a very small number of samples in your data set, I would say you should be fine to remove them and just continue your analysis on the remainder of your samples that have much higher read counts.

Hope this helps!

Cheers :lizard:

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