Extract tree used to create deblurred biom from deblurred biom artifact

[Stephanieorch (Stephanie Orchanian)]

I have a deblurred reference hit biom table in Qiita but have no biom tables prior to that (I combined a few studies so I only have the combined reference hit artifact). Is there a way to extract the tree used or the representative sequences from deblurred biom table from the artifact so I can use it in my Qiime2 commands?

I’ve tried doing this on my own by importing my biom table and then using the imported .qza to create a tree but I get an error.

I import the biom using this command:

qiime tools import \
  --input-path table.NEWfrom_txt_hdf5.biom \
  --type 'FeatureTable[Frequency]' \
  --source-format BIOMV210Format \
  --output-path feature-table-2.qza

then I run the 1st command to start building the tree:

qiime alignment mafft \
  --i-sequences feature-table-2.qza \
  --o-alignment aligned-rep-seqs.qza

and got this error:

Plugin error from alignment: Argument to parameter ‘sequences’ is not a subtype of FeatureData[Sequence].

[colinbrislawn (Colin J Brislawn)]

Great question! I know that you can use the greengenes tree for closed-ref OTU picking, but I would also like to know how to find or build the tree for deblur.

Colin

[antgonza (Antonio Gonzalez Pena)]

Hello,

I think this was answered here:

Importing deblur data from QIITA

I’m working on a meta-analysis of datasets from QIITA for analysis in qiime2. I’ve been able to download datasets processed using deblur from QIITA as well as their respective metadata files. I’ve merged the BIOM and metadata files but in order to continue with my analysis, I require a rep-seqs file. It looks like this file isn’t generated by QIITA from data processed with Deblur. Is there a way I could extract the rep-seqs file from the deblur BIOM file in order to run “qiime diversty core-metr…

Could you confirm?

Thanks!

[Stephanieorch (Stephanie Orchanian)]

It seems this just made all of the sequences capitalized. I want to import the deblurred reference hit biom table into qiime2 then use it to make a tree.

[antgonza (Antonio Gonzalez Pena)]

Hi @Stephanieorch,

Thank you for updating your original question and adding your commands; now I have a better idea of what the confusion is.

Basically, to generate a tree you need to use the sequences, not the biom table, which your second command is doing. To get the sequences from your biom, you need to follow the command here: Importing deblur data from QIITA, once you have your sequences you can import them as a new artifact type FeatureData[Sequence], which will be the input of your second command.

Hope this helps.