merge biom files taxononomy files

[oatesa1]

Ive have followed the following info Merge biom files to import biom and taxonomy files from each biom file i want to merge. I have been able to merge the biom files using qiime feature-table merge. I dont know if i should be merging the taxononomy files too and if so how?

[Nicholas_Bokulich]

Welcome @oatesa1! Have you seen the merge-taxa action in the feature-table plugin?

$ qiime feature-table merge-taxa --help
Usage: qiime feature-table merge-taxa [OPTIONS]

  Combines a pair of feature data objects which may or may not contain data
  for the same features. If different feature data is present for the same
  feature id in the inputs, the data from the first will be propagated to
  the result.

Options:
  --i-data MULTIPLE ARTIFACT PATH List[FeatureData[Taxonomy]]
                                  The collection of feature taxonomies to be
                                  merged.  [required]
  --o-merged-data ARTIFACT PATH FeatureData[Taxonomy]
                                  The resulting collection of feature
                                  taxonomies containing all feature taxonomies
                                  provided.  [required if not passing
                                  --output-dir]
  --output-dir DIRECTORY          Output unspecified results to a directory
  --cmd-config FILE               Use config file for command options
  --verbose                       Display verbose output to stdout and/or
                                  stderr during execution of this action.
                                  [default: False]
  --quiet                         Silence output if execution is successful
                                  (silence is golden).  [default: False]
  --citations                     Show citations and exit.
  --help                          Show this message and exit.

[mefistofele82]

Hi,

yes, you have to import taxonomy separately, as Qiime2 artifacts, and then merge all together with:

qiime feature-table merge-taxa
–i-data XXXXXXX_FASTQ_SSU_OTUtaxonomy.qza
–i-data YYYYYYY_FASTQ_SSU_OTUtaxonomy.qza
–o-merged-data merged_taxonomy.qza