for rep-seqs.qza and table.qza what shold I choose

[yogurt]

Hi I've just started analyzing COI and I am a beginner.

I followed every tutorials and I just had a question.

In the input format there were always rep-seqs.qza and table.qza. But I get those files after denoising and clustering and also after when chimera was filtered.

For example, in the 'test the classifier' step
$qiime feature-classifier classify-sklearn
--i-classifier classifier.qza
--i-reads rep-seqs.qza
--o-classification taxonomy.qza
for the 'rep-seqs.qza', should I put rep-seps from denoised result? or chimera filtered rep-seqs? or denovo clustered rep-seqs?

Thank you for the answer

[SoilRotifer (Mike Robeson)]

Hi @yogurt, welcome to :qiime2:!

What commands have you run prior to this step? Which tutorials were you following? There are several...

It would appear to me that you'd want to classify your OTU clustered reads, i.e. whichever data you will actually use in your downstream analysis.

-Mike

[yogurt]

Thank you for the reply Mike!
I got artifacts from denoise/cluster step which are Feature Table and Representative Sequence.

In many sites, the input format of FeatureTable[Frequency] seems like Table.qza and FeatureData[Sequence] seems like rep-seq.qza.

1. For the taxonomy classification
   $qiime feature-classifier classify-consensus-blast\
   --i-query rep-seqs.qza \
   --i-reference-reads HOMD.fasta.qza \
   --i-reference-taxonomy HOMD.taxonomy.qza \
   --o-classification blast-taxonomy.qza

the input file is rep-seq.qza. I put rep-seq.qza from denoise/cluster output file. Is this right?

2. Alignment and Phylogeny the input formation is FeatureData[Sequence] and FeatureTable[Frequency]. Are those files are from denoise/cluster step?

3. Further analysis eg. alpha, beta diversity, should I use FeatureData and FeatureTable from denoise/cluster step?

Thank you!

[SoilRotifer (Mike Robeson)]

@yogurt

1. For the taxonomy classification
   $qiime feature-classifier classify-consensus-blast
   –i-query rep-seqs.qza
   –i-reference-reads HOMD.fasta.qza
   –i-reference-taxonomy HOMD.taxonomy.qza
   –o-classification blast-taxonomy.qza

the input file is rep-seq.qza. I put rep-seq.qza from denoise/cluster output file. Is this right?

Yes, as I mentioned previously, whichever data you will actually use in your downstream analysis. If you'd like to use your denoised and clustered reads, then this is what you'd use. .

@yogurt

Alignment and Phylogeny the input formation is FeatureData[Sequence] and FeatureTable[Frequency]. Are those files are from denoise/cluster step?

As outlined in our online documentation, If you add --help to any of the qiime commands, you'll see the help text. This will inform you of the input and output types, e.g. FeatureData[Sequence]. For example, when I type:

qiime phylogeny align-to-tree-mafft-raxml --help 

You will see that the input for this pipeline is FeatureData[Sequence], and the output consists of several files:

• alignment: FeatureData[AlignedSequence]
• masked alignment: FeatureData[AlignedSequence]
• tree: Phylogeny[Unrooted]
• rooted tree Phylogeny[Rooted]

@yogurt

Further analysis eg. alpha, beta diversity, should I use FeatureData and FeatureTable from denoise/cluster step?

As mentioned above, you can determine the input and output types by using --help. I suggest you work through the tutorials. The Moving Pictures and Parkinson's tutorials contain many steps used in a typical analyses, regardless of the amplicon / gene you are analyzing. They provide many examples of what you are tying to do.

-Mike