Deblur Visualizations Aid

[Sirtaj-Singh]

Good Afternoon,

I was hoping I could get some more information about accessing the summary statistics when using Deblur. Here is what the first tutorial has to say about it:
“The two commands used in this section generate QIIME 2 artifacts containing summary statistics. To view those summary statistics, you can visualize them using qiime quality-filter visualize-stats and qiime deblur visualize-stats, respectively.”

How do I use those lines of code?

As a side question, what are the communities thoughts on using DADA2 versus Deblur?

Thank you in advance!

[thermokarst]

Hi @Sirtaj-Singh,

How do I use those lines of code?

Assuming you are following along with the Moving Pictures tutorial, in the quality control step, you should have run commands similar to these two:

$ qiime quality-filter q-score \
 --i-demux demux.qza \
 --o-filtered-sequences demux-filtered.qza \
 --o-filter-stats demux-filter-stats.qza

$ qiime deblur denoise-16S \
  --i-demultiplexed-seqs demux-filtered.qza \
  --p-trim-length 120 \
  --o-representative-sequences rep-seqs-deblur.qza \
  --o-table table-deblur.qza \
  --o-stats deblur-stats.qza

If you wish to view the summary statistics, there are two ways to get at that:

$ qiime quality-filter visualize-stats \
  --i-filter-stats demux-filter-stats.qza \
  --o-visualization demux-filter-stats.qzv

or

$ qiime deblur visualize-stats \
  --i-deblur-stats deblur-stats.qza \
  --o-visualization deblur-stats.qzv

Once you have the outputs (either demux-filter-stats.qzv or deblur-stats.qzv), you can view them with https://view.qiime2.org, or by running qiime tools view FILENAME.QZV.

As a side question, what are the communities thoughts on using DADA2 versus Deblur?

Maybe you could ask on BioStars or SEQanswers?

Hope that helps!

[Sirtaj-Singh]

I see, the code you posted regarding viewing the summary statistics really helped! Thank you!

I did not know such vast forums existed, much appreciated!