assign_taxonomy.py questions

[sdpapet]

Hello, I'd like to use RDP database to assign taxonomy to my OTU table. I download it RDP dabase from the website--see attach file.

The package include two files: one is fasta file and the other is taxonomic info. However, unlike default green gene database, it doesn't offer fasta file and taxonomic info at different cut off -- for example 95, 97? Can I use this file directly?

Also, the assign_taxonomy.py default method is uclust? If I use RDP database, can I still use uclust? Or I have to change -m option RDP too?

Thanks,
Ben

[Colin Brislawn]

Hello Ben,

Using other databases with qiime can be tricky, and there will be a lot of work you will have to tackle independently. If you want to try it, this page outlines the format of a qiime compatible database. 

http://qiime.org/documentation/file_formats.html#sequence-id-to-taxonomy-mapping-files 

Looking at the provided files in the greengenes database also provide a good example of the valid format. 

 doesn't offer fasta file and taxonomic info at different cut off -- for example 95, 97? Can I use this file directly? 

Yes, you should be able to use them directly. 

Also, the assign_taxonomy.py default method is uclust? If I use RDP database, can I still use uclust?

Yes, you can still use uclust as the assignment algorithm with any database in a valid format, including the RDP database.

Colin

[sdpapet]

Hi Colin,

Thanks, just make sure I got this correct. The website says "ID-to-taxonomy maps are pass to assign_taxonomy.py -m blast via the -t/--id_to_taxonomy_fp option with an associated fasta file passed via -r/--reference_seqs_fp."

This means, I can only use the -m blast, not uclust or other methods, if I use other databases.

Thanks,
Ben

[Colin Brislawn]

Hello Ben,

Here, -m blast is just used as an example of an algorithm. You could also use -m uclust or -m rdp. 

Not matter which algorithm you use, you will still have to pass both -t and -r in order to use a non-default database. 

Perhaps the full documentation for assign_taxonomy.py would be helpful here.

http://qiime.org/scripts/assign_taxonomy.html

Colin

[Maria]

Hi Ben,

This sounds interest to me! Did you used? It worked for you?

Also, where did you find this document in the RDP?

Thank you! I will try it with my analysis!

Maria