dada2 Sequence quality control

[DKZ]

Hi, everyone
I am using QIIME2 2019.1 on server， system：Linux Ubuntu 16.04 LTS.
I used dada2 to quality control，and too many sequences were filtered, i am not sure whether my data quality is too bad or my parameter settings are wrong.
my command and results see as follow:
qiime dada2 denoise-single
--i-demultiplexed-seqs single-end-colon-demux.qza
--p-trim-left 0
--p-trunc-len 450
--o-representative-sequences rep-seqs.qza
--o-table table.qza
--o-denoising-stats stats.qza

thanks for any reply!

[thermokarst]

Hi @DKZ!

@DKZ

i am not sure whether my data quality is too bad or my parameter settings are wrong.

Good questions! We can't really help with that though unless we have something like the demux summarize visualization on hand to contextualize the command run, and the stats provided. Thanks!

[DKZ]

thank you so much, here are my data informations and command

data format: joined paired-end sequences (obtained from sequencing company）

data import command：
qiime tools import
--type 'SampleData[SequencesWithQuality]'
--input-path colon-manifest.csv
--output-path single-end-colon-demux.qza
--input-format SingleEndFastqManifestPhred33
qiime demux summarize
--i-data single-end-colon-demux.qza
--o-visualization demux.qzv
qiime tools view demux.qzv

thanks again.

[thermokarst]

Is this iontorrent data? If so, you could try out denoise-pyro in DADA2 - this is tuned for pyrosequencing data ().

[DKZ]

thanks for your help.