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,
Calum
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