Hi, I'm very new to QIIME, so apologies for this trivial question.
I'm using QIIME2/2022.8 and got this result (see screenshot) after I removed the primers using this code:
qiime cutadapt trim-single --i-demultiplexed-sequences reads_qza_fwd/reads_fwd.qza --p-cores 1--p-front GTGCCAGCMGCCGCGGTAA --o-trimmed-sequences reads_qza_fwd/reads_trimmed_fwd.qza
I don't seen any box plots, is this normal?
It's not expected, but it might be OK!
What machine did you use for sequencing? Illumina MiSeq, or Illumina NovaSeq, or something else?
Thanks, Colin! Illumina HiSeq was used for this one.
EDIT: Some new Illumina machines and sequencing chemistries use binned quality scores. NovaSeq does but I'm not sure about older ones like HiSeq. 
See this form post and associated issue on GitHub.
Ah, that explains it: HiSeq uses Illumina's new binned quality scores.
You could try running your reads through DADA2. If does not work try deblur.
All right, I'll try those, hope one of them works. Thanks again!
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