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!
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!
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
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
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
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
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?
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
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.
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