Selecting parameters for DADA2


I am new to QIIME and trying to learn how to use it. I have gone through the tutorials and now I am trying to run some basic analysis to get the hang of it.
So far, I have successfully imported data in QIIME using the manifest format, where the title of each file is the barcode, and I should now run the denoising step. I have a few basic questions:

i) since I have not done the demultiplexing in QIIME 2, how can I create an interactive quality plot in order to select the parameters for dada2?
ii) is there another way of choosing the parameters?
iii) would it be possible to demultiplex sequences in QIIME 2 to get the quality plot if they are not in EMP format?

Alex :slightly_smiling_face:

if you imported via the manifest format (with each sample originally in its own fastq file), then creating a visualization of you demux file should show you an interactive quality plot. So you imported with a code similar to this?

qiime tools import \
--type 'SampleData[PairedEndSequencesWithQuality]' \
--input-path Manifest.csv \
--output-path Demux.qza \
--source-format PairedEndFastqManifestPhred33

This makes you Demux.qza file which you can then visualize using:

 qiime demux summarize \
--i-data Demux.qza \
--o-visualization Demux.qzv

Then open and drag and drop it into the box and click interactive quality plot button at the top.

Does that work?


A reply has been split into a new topic: Feature-table summarize metadata index problem

This topic was automatically closed 31 days after the last reply. New replies are no longer allowed.