Grouping sequences by metadata?

feature-table
(Jill Adkins) #1

Hello,

I am attempting to filter my sequences using my metadata file but I am getting an error message that says all the features have been filtered out of the data. I have three different study groups composed of about 22 samples each. I want to determine the relative abundance of phyla in each group as opposed to the relative abundance in each individual sample. I might be going about this the wrong way so any feedback is much appreciated.

To filter sequences I used:

qiime feature-table filter-seqs \

–i-data rep-seqs.qza
–m-metadata-file ‘validatedALLM1 - Sheet3.tsv’
–p-where “‘sample id’=‘C’”
–o-filtered-data rep-seqs-C.qza
–verbose

This is the output I get:

(qiime2-2019.1) [email protected]:~/M1alloutput$ qiime feature-table filter-seqs --i-data rep-seqs.qza --m-metadata-file ‘validatedALLM1 - Sheet3.tsv’ --p-where “‘sample id’=‘C’” --o-filtered-data rep-seqsC.qza --verbose
Traceback (most recent call last):
File “/home/ubuntu/miniconda3/envs/qiime2-2019.1/lib/python3.6/site-packages/q2cli/commands.py”, line 274, in call
results = action(**arguments)
File “</home/ubuntu/miniconda3/envs/qiime2-2019.1/lib/python3.6/site-packages/decorator.py:decorator-gen-318>”, line 2, in filter_seqs
File “/home/ubuntu/miniconda3/envs/qiime2-2019.1/lib/python3.6/site-packages/qiime2/sdk/action.py”, line 231, in bound_callable
output_types, provenance)
File “/home/ubuntu/miniconda3/envs/qiime2-2019.1/lib/python3.6/site-packages/qiime2/sdk/action.py”, line 365, in callable_executor
output_views = self._callable(**view_args)
File “/home/ubuntu/miniconda3/envs/qiime2-2019.1/lib/python3.6/site-packages/q2_feature_table/_filter.py”, line 112, in filter_seqs
raise ValueError(‘All features were filtered out of the data.’)
ValueError: All features were filtered out of the data.

Plugin error from feature-table:

All features were filtered out of the data.

See above for debug info.

Should I be using a different feature to filter my sequences? Or is there a way I can use the relative abundance data I have already generated for each of my samples to look at the relative abundance of phyla in each of the groups?

Thank you in advance for your help!

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(Mehrbod Estaki) #2

Hi @Jill_Adkins,
Hmm, that error message is odd to me. The approach you are describing shouldn’t even work at all because you are providing a rep-seq artifact that holds no information regarding your samples, and a metadata parameter that couldn’t possibly provide a list of features to filter from that rep-seqs. So I don’t know why anything is filtered at all. Anyways, that’s not your issue here :stuck_out_tongue:

I think what you want instead is the feature-table group function for a way to combine your samples based on a metadata category. Then you can plot these as groups. However, I do believe you’ll have to use your frequency table before you converted it to relative abundances. Though, it would be nice if group could also accept FeatureTable(RelativeFrequency).

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(Jill Adkins) #3

Thank you for the quick response @Mehrbod_Estaki!

I knew I was doing something silly! Feature-table group worked! Thank you so much for your help!

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