How to exclude certain kingdom

User Support
1

Hi,

I am processing my 16S data. My primer is archaea specific, but the final taxonomy file contains bacteria. May I ask how to exclude bacteria or how to exclude certain kingdom?

Thanks a lot

2

By the way, I used the latest Silva 132 classifier, it is very good!

1 Like
3

Hey @Harry,

Check out these two commands:

qiime taxa filter-seqs
qiime taxa filter-table

You should be able to use either/both. You can also replicate the behavior with normal filtering and a --p-where clause, but the two commands above are easier to use.

1 Like
4

Thanks a lot, it works!

Please allow me to upload my protocol:

First of all, upgrade to qiime2-2018.4

Download the latest Silva 132 qiime compatible full-length classifier.
Please download at: Silva 132 classifiers
(Silva 132 99% OTUs (full-length, seven-level taxonomy) )

Using the command:
qiime feature-classifier classify-sklearn --i-classifier silva-132-99-nb-classifier.qza --i-reads YourRepSeqsFromDada2.qza --o-classification taxonomy.qza

Next step is to exclude sequences that your primer does not target, e.g., for archaea specific primers, you should exclude mitochondria, chloroplast, bacteria. Use the command:
qiime taxa filter-table --i-table YourTableFromDada2.qza --i-taxonomy taxonomy.qza --p-exclude bacteria,chloroplast,mitochondria,eukaryota --o-filtered-table table-filtered.qza,

final step, visualize it: (please note that metadata file MUST be in TSV format)
qiime taxa barplot --i-table table-filtered.qza --i-taxonomy taxonomy.qza --o-visualization filterred-txonomy.qzv --m-metadata-file YourMetadataFile.tsv

1 Like
5

This topic was automatically closed 31 days after the last reply. New replies are no longer allowed.