Importing open reference dataset

[arnon (Arnon Lieber)]

I’m looking to import the data produced by the pick_open_reference_otus.py protocol from QIIME 1.9.1. Are there any pointers or tutorials in which files to import from the open reference protocol? The folder output shows a number of .fna, .tre and .biom files and it is not clear to me which files I need to import.

I can see the specific commands to import the representative sequences and BIOM tables, however I’m confused as to which files I need to import from QIIME 1.9.1

[thermokarst]

Hi @arnon!

What is it you would like to do with these data in QIIME 2? Examples for importing the bio and tre files can be found here:

• Importing data — QIIME 2 2018.4.0 documentation
• Importing data — QIIME 2 2018.4.0 documentation

I am not familiar with the specifics of the files output from this script in QIIME 1, but I imagine that the biom tables are annotated with sequence info - you can import that as a FeatureData[Sequence] artifact from your BIOM table:

Feature-table filter-samples removes taxonomy from biom table

Hi @antgonza! Looks like you found a bug! Our general strategy with BIOM tables is to normalize them on read/write, so that these biom metadata fields are stripped out (more on that below). It looks like this normalization is skipped when importing BIOMV210Format files (the normalization is applied when importing BIOMV100Format, though). As far as "stripping out biom metadata", the idea here is that we can represent these data using other QIIME 2 semantic types, for example the taxonomy metad…

Hope that helps! Keep us posted! :qiime2:

[yoshiki (Yoshiki Vázquez Baeza)]

@arnon, I just went through the ouputs of pick_open_reference_otus.py from QIIME 1.9.1, the files that you want to look at are:

• OTU taxonomic assignments: rep_set_tax_assignments.txt
• OTU table exluding OTUs with fewer than 2 sequences and sequences that fail to align with PyNAST and including OTU taxonomy assignments: otu_table_mc2_w_tax_no_pynast_failures.biom.
• OTU phylogenetic tree: rep_set.tre.
• New reference sequences (i.e., OTU representative sequences plus input reference sequences): new_refseqs.fna.

These are the specific commands I executed (from the links that @thermokarst posted).

qiime tools import \
--input-path new_refseqs.fna \
--output-path representative-sequences.qza \
--type FeatureData[Sequence]

qiime tools import \
--input-path rep_set.tre \
--output-path unrooted-tree.qza \
--type Phylogeny[Unrooted]

qiime tools import \
--input-path otu_table_mc2_w_tax_no_pynast_failures.biom \
--output-path feature-table.qza \
--type FeatureTable[Frequency]

# the source format may need to be --source-format BIOMV100Format if you were using an older version of QIIME
qiime tools import \
--input-path otu_table_mc2_w_tax_no_pynast_failures.biom \
--output-path taxonomy.qza \
--type FeatureData[Taxonomy] \
--source-format BIOMV210Format

After doing this, I looked at the data using QIIME2. I ran core-metrics phylogenetic and created a stacked barplot. Hopefully this helps @arnon.

[arnon (Arnon Lieber)]

Thank you Yoshiki!
I’ll give it a try and let you know if it works for me.

[arnon (Arnon Lieber)]

Dear Yoshiki,Thermokrast,

Unfortunately it didn’t work. Something is still wrong. Any idea how to work around it?

Thank you,
Arnon

[thermokarst]

Hey there @arnon, we will need a little more info before we can really help. Can you help us understand what didn't work by providing:

• What version of QIIME 2 are you running?
• What were the exact command or commands you ran? Copy and paste.
• What was the error you observed, if applicable?
• What was the desired result, and how did that differ from the observed result?

Thanks! :qiime2: