How to get species level classification of only first 2 stages of Qiime analyzed sequenced data?

Dear Friends,

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!

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Good afternoon,

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 --o-filtered-table Ionexpress_1to11-dada2-rep-seqs-table2-filtered-2.qza --verbose

Try that

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Hello Daniel,

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! :slight_smile:


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