Interactive Quality Plot”. Il Middle of box-50th (Median)

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1

Hi,
I genereted my demux.qzv and I insert it in https://view.qiime2.org to evaluate the quality of the reads. However, the value of Il Middle of box-50th (Median) is under of range 30-40. How will I do? Have I to run (16S Illumina-faecal samples) another time all samples ?

thanks

2

Hello CARMEN,

Because the quality drops at this point, you could truncate your reads at that point when running DADA2. See this example from the Atacama soil microbiome tutorial.

qiime dada2 denoise-paired \
  --i-demultiplexed-seqs demux.qza \
  --p-trim-left-f 13 \
  --p-trim-left-r 13 \
  --p-trunc-len-f 150 \
  --p-trunc-len-r 150 \
  --o-table table.qza \
  --o-representative-sequences rep-seqs.qza \
  --o-denoising-stats denoising-stats.qza

Those --p-trim-left and --p-trunc-len settings were chosen by looking at the quality plots.

Q-scores of 30-40 is still pretty good (99.9% - 99.99% accurate!) so you could use a slightly longer trunc len setting too!

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