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

[DECARO (CARMEN)]

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

[colinbrislawn (Colin J Brislawn)]

Hello CARMEN,

@DECARO

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 ?

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!