How to map taxonomy to OTUs

Question

[xioli2013]

Hi,

I have encountered an issue that I was trying to map taxonomy to an otu table. The barcode is trnL. I have managed to get all viridiplantae trnL sequences from NCBI as a database for local blast, and the associated lineage to each sequence entry. Also I have the representative sequences by vsearch. I wonder if there is a way to create the id_to_taxonomy.txt file as in assign_taxonomy.py in qiime.

thank you,

xio

[Trombone Engineer]

What IDs are your OTUs? If you are using Green Genes, you can look at the precalculated file for your percent similarity (i.e. 97%) and see the complete list of IDs and taxonomy. Are you using QIIME to use assign_taxonomy.py or is there a reason you are using a different method? Local blast can be helpful and accurate but is much slower than QIIME or a similar method.

[xioli2013]

Thanks for the reply. I am using trnL as described in the question. I have solved the issue now.

Answer 1

[xioli2013]

I have solved the issue by creating right formatted id_to_taxonomy table and fed it to assign_taxonomy.py in QIIMME, which worked.