Taxonomy Assignment with RDP Classifier

Other Bioinformatics Tools
1

Hi there,

I have a fasta file with sample OTUs and would like to annotate this fasta file to produce a new fasta file. It is like the function in Qiime1:
assign_taxonomy.py -i pacbio_otu.fasta -m rdp

I have Qiime 2 on Virtualbox and cannot find a way to do the same for this particular fasta file. Do you have any advice for my situation?

Many thanks!

2

Hello @YinXun, this part of the Moving Picture tutorial discusses how to use classify-sklearn in QIIME 2. It behaves very similarly to assign_taxonomy.py in QIIME. It doesn't output a new fasta file though. It, like assign_taxonomy.py, outputs a metadata file. Do you need the annotations added specifically to the fasta file for any reason?

3

Hello there,

Thanks for your response. I am looking to have taxonomy annotation on my pacbio_otu.fasta file as I would like to build my own taxonomy database.

Eventually, I will have this taxonomy database in fasta format, so I could run sintax with other datasets against it. I have downloaded the RDP training set from sintax (SINTAX downloads) for my case.

Do you have any advice with what I can do for this? Many thanks!

Zach

6

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