I have analyzed 10 samples of water using QIIME. I have the taxa composition like phyla level till species level for all 10 samples by performing QIIME analysis. Is there a way, I can get the taxa classification information only for the first 2 samples from the analyzed results? Thanks!
I think you could do this using
qiime feature-table filter-samples. You can learn more about this here:
Once you have filtered to just the 2 samples you want, you can make the graphs again.
Thanks @colinbrislawn: I did this:
qiime feature-table filter-samples --i-table Ionexpress_1to11-dada2-rep-seqs-table2.qza --m-metadata-file cDNA_1to11_metadat.tsv --p-where ww1cDNA ww2cDNA --o-filtered-table Ionexpress_1to11-dada2-rep-seqs-table2-filtered-2.qza --verbose
I am looking to retain only "ww1cDNA" and "ww2cDNA" SampleIDs, but it gives this error:
There was a problem with the command:
(1/1) Got unexpected extra argument (ww2cDNA)
How can I filter two samples at one time? thanks!
My metadata file is: cDNA_1to11_metadat.tsv (1.2 KB)
Filter using the mapping file only.
cDNA_1to11_metadat_onlyww1andww1.txt (458 Bytes)
qiime feature-table filter-samples --i-table Ionexpress_1to11-dada2-rep-seqs-table2.qza --m-metadata-file put.metadata.file.here.txt --o-filtered-table Ionexpress_1to11-dada2-rep-seqs-table2-filtered-2.qza --verbose
So close! The
--p-where command needs a specific syntax and I bet that will fix your command.
There is a great example in this post, which is a great example:
--p-where "BodySite='gut' AND Year='2008' AND Subject='subject-1'"
For your data, it might look like this:
--p-where "[#SampleID]='ww1cDNA' OR [#SampleID]='ww2cDNA'"
EDIT: I’ve updated the command you could try on your data. Let me know how it works!
Thanks @thermokarst and @colinbrislawn. It works now!
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