Dereplicating a SampleData[Sequences] artefact

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

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!

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

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

2 Likes

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