Qiime2 workflow

Hi, qiime2 is a beginner.
I use paired-end seq data from illumina miseq.
Human intestinal microbial data is 16s ampliconsequencing.
I am curious about the workflow until OTU generation.

  1. importing data ->qza

  2. demultiplexing -> demux.qza

  3. qualitycontrol
    r = 3, q ​​= 3, p = 0.75, n = o, c = 0.05 -> demux-filtered.qza
    We have progressed to this point.

  4. At what stage does cutadapt go?

  5. How does demultiplexing replace the completed fastq file with a qza file?

  6. Is it correct to proceed with dada2 or deblur after proceeding to the present?

  7. demux-filtered.qza. What is the command to move dada2 to a file?

  8. Do you proceed with merge after denoise in dada2?

  9. What if I try to use a database other than greengene data?

  10. Do you generate otu via vsearch with the output of dada2? What is the command? 8. What is the format of the otu file?

I am wandering a lot with the first time.
Please give detailed explanation.
Thank you.

Hello @kimshinseung,

Thanks for using Qiime 2! Welcome! :qiime2:

These are all really good questions, which is why they are covered in detail in the "Moving Pictures" tutorial. This tutorial shows a full qiime 2 pipeline, and you can compare this to the pipeline you described here. I think that once you have done the "Moving Pictures" tutorial, the order of steps will be more clear.

Qiime 2 makes use of new file types (.qza and .qzv) and I notice you have questions about those too. These are covered in detail here:

Let me know once you have finished the “Moving Pictures” tutorial or if you have any questions along the way.



Thank you for answer.

  1. Is the otu table in qiime1 the same as the feature table?
  2. Is a database like greengene used in --m- below?
    ------------------------------------------------ qiime feature -table summarize
    –i-table table.qza
    –o-visualization table.qzv
    –m-sample-metadata-file sample-metadata.tsv
    qiime feature-table tabulate-seqs
    –i-data rep-seqs.qza
    –o-visualization rep-seqs.qzv
  3. Does the trim-length of the deblur mean the minimum length of the faired-end seq to overlap the library size? Is this process a merge process?

Thank you

Yes. The features in the feature table could be OTUs or AVSs.

Nope. That’s for the --m-sample-metadata-file.
That’s the first thing explained in the Moving Picture tutorial. Have you done the tutorial yet? :wink:

From the Moving Picture Tutorial:

Next, the Deblur workflow is applied using the qiime deblur denoise-16S method. This method requires one parameter that is used in quality filtering, --p-trim-length n which truncates the sequences at position n .

I think so many of your questions will be answered when you do the tutorial! You will learn so much!



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