Change default levels of taxonomic ranks classified

[syrenawhitner]

Hi there,

I'm working if you can change the default number of taxonomic levels used when clustering/annotating? QIIMEs default is 7, but my database (PR2) uses 9 taxonomic levels so am trying to find an easier way around this beyond reformatting my entire database.

I am also very broadly wondering if anybody has experience using the PR2 database in QIIME to assign taxonomy to rRNA reads extracted from metatranscriptomic datasets? if so please reach out as I have been getting a lot of interesting results but having a hard time finding resources online..

Thanks!

[SoilRotifer (Mike Robeson)]

Hi @syrenawhitner,

You can use as many taxonomic ranks as you'd like. As long as the ranks are delimited by a ;, and have the same number of ranks for each taxa, you'll be fine.

For example, you can use RESCRIPt to make a SILVA or GenBank databases with 5 ranks, 9 ranks, 14 ranks, etc...