rarefaction data

Hi,

Anyone knows how to have access to the rarefied data? I mean, when we do the rarefaction, it is possible to see those files, for example per species?

Thank you!

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Hi @annsantos,

You should be able to find this in your rarified table. If you’re running core diversity, this post may be helpful in locating that file.

Best,
Justine

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Hi!
Thank you for your reply. However i couldn’t find what i was looking for, unfortunately.

Maybe i didn’t explained myself as i should. What i need is the rarefied data because i want to compare the counts for each specie with the relative abundance. Basically i want to see if i get the same tendency.

Hi @annsantos,

If you ran core diversity, the rarified table is in core-metrics-results/rarefied_table.qza (like in the post I linked.)

Best,
Justine

2 Likes

Thank you!

I got it! Now, do you know how can i have a table with those counts per taxa?

Ana Santos

You can collapse a rarefied take in the same way that you collapse any other table, with qiime feature-table group where you use your taxonomy qza as your metadata and set --p-axis as feature. I think you can set the level --m-metadata-column, but you might need to play with that.

Best,
Justine

Hi,

Since that the taxonomy file is not a table, how i find out the column for the -m-metadata-column?

Thank you

Hi @annsantos,

As a brilliant collegue suggested to me, you may find more success with

qiime taxa collapse

I apologize, I often work with my taxonomy as metadata, particularly, in the python API so thats often a way I think of it.

Best,
Justine

1 Like

qiime taxa collapse
–i-table where i put the rarefied data?
–i-taxonomy and here the taxonomy table?
–p-level 7 \ #species level
–o-collapsed-table species-table.qza

Thank you

Hi @annsantos,

I wanted to walk you through how I do this to check this. So, I pulled up the help documentation.

qiime taxa collapse --help
Usage: qiime taxa collapse [OPTIONS]

  Collapse groups of features that have the same taxonomic assignment
  through the specified level. The frequencies of all features will be
  summed when they are collapsed.

Inputs:
  --i-table ARTIFACT FeatureTable[Frequency]
                         Feature table to be collapsed.             [required]
  --i-taxonomy ARTIFACT FeatureData[Taxonomy]
                         Taxonomic annotations for features in the provided
                         feature table. All features in the feature table must
                         have a corresponding taxonomic annotation. Taxonomic
                         annotations that are not present in the feature table
                         will be ignored.                           [required]
Parameters:
  --p-level INTEGER      The taxonomic level at which the features should be
                         collapsed. All ouput features will have exactly this
                         many levels of taxonomic annotation.       [required]
Outputs:
  --o-collapsed-table ARTIFACT FeatureTable[Frequency]
                         The resulting feature table, where all features are
                         now taxonomic annotations with the user-specified
                         number of levels.                          [required]
Miscellaneous:
  --output-dir PATH      Output unspecified results to a directory
  --verbose / --quiet    Display verbose output to stdout and/or stderr
                         during execution of this action. Or silence output if
                         execution is successful (silence is golden).
  --citations            Show citations and exit.
  --help                 Show this message and exit.

The ---i-table flag is supposed to be for a FeatureTable Artifact, and the --i-taxonomy should be for a taxonomy artifact, so those are the inputs I would expect?

The one thing Im not sure about about is whether the taxonomy counts from 1 or 0. So, you may get an error with 7 (in which case try 6).

Best,
Justine

4 Likes

Thank you!

So, to recap:

1- I did the qiime feature-table rarefy;
2 - qiime rate collapse
–i-table rarefied / rarefied-table1973.qzv
–i-taxonomy taxonomy.qza
–p-level 7
–o-collapsed-table species-rarefied-table.qza

Now, how do I convert in qza? Or is it better to tsv?

2 Likes

Hi @annsantos,

Yes, that looks good. Your output table looks like it’s already a qza, so Im not sure what you mean about conversion?

Best,
Justine

1 Like

I’m sorry, i meant to say qzv.

Hi @annsantos,

Now this behaves like any collapsed feature table. If you want to do the line-by-line comparison, your best bet is probably to take it out of QIIME.

Best,
Justine

My first analyse was to check the relative frequencies of my taxa (per class, genus and species). What i did was :

1)qiime taxa collapse
2) qiime feature-table relative-frequency
3) qiime tools export
4) biom convert (to tsv)

Now, i want to do the same thing but with counts.

Hi @annsantos,

Then, yes, that should work as a pipeline.

Best,
Justine

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