Dereplicating a SampleData[Sequences] artefact

User Support
#1

Hi everyone;

I have a seq.fna file from a QIIME1 project and I want to work with it as input file for QIIME2 workflow. In the tutorial "Clustering sequences into OTUs using q2-vsearch"I found how to do it, but the example presented there works with 2 input files:
85_otus.qza
seqs.fna

My question is: I have the seqs.fna file from Qiime1, but I don’t realize where is the other file that looks like to 85_otus.qza. Where can I find it? Or which one data can I build it?

Thank you in advance.

Ro

#2

That file is just some reference sequences that have been imported into QIIME 2. You can download from Greengenes or Silva as linked from here and import as a FeatureData[Sequence] artifact.

I hope that helps!

#3

Thank you very much for your advance. I could import as .qza artefact the 85_otus file from the rep_set_aligned folder from the gg_13_8_otus.tar.gz file, with:

qiime tools import \

–input-path 85_otus.fasta
–output-path 85_otus.qza
–type ‘FeatureData[Sequence]’

But I couldn’t import the seqs.fna file into a .qza artefact.
I tried with:

qiime tools import \

–input-path seqs.fna
–output-path seqs.qza
–type ‘FeatureData[Sequence]’

And give an error:

There was a problem importing seqs.fna:

seqs.fna is not a(n) DNAFASTAFormat file

I also tried with:

qiime tools import \

–input-path seqs.fna
–output-path seqs.qza
–type ‘SampleData[Sequences]’

And give the error:

There was a problem importing seqs.fna:

seqs.fna is not a(n) QIIME1DemuxFormat file

I’m sure that seqs.fna file must be the file that I need to use, because is the file that was used in QIIME1 analysis that I want replicate.
What can I do?
Help?
Thanks a lot

Ro

#4

I don’t realice what Idid, but worked!!!
I executed your advice in Seqs.fna is not a(n) QIIME1DemuxFormat file.

I executed:

cat seqs.fna | tr 'acgt' 'ACGT' > new_seqs.fna

qiime tools import \
   --input-path new_seqs.fna \
   --output-path seqs.qza \
   --type SampleData[Sequences]

And its created the files:
new_seqs.fna
seqs.qza
-type
-input-path
-ouput-path

The last 3 files are empty.

Thanks for your help!!

Ro

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#5

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