How to map taxonomy to OTUs
1
0
Entering edit mode
3.8 years ago
xioli2013 ▴ 10

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

trnL otu taxonomy table • 1.4k views
ADD COMMENT
0
Entering edit mode

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.

ADD REPLY
0
Entering edit mode

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

ADD REPLY
1
Entering edit mode
3.8 years ago
xioli2013 ▴ 10

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

ADD COMMENT

Login before adding your answer.

Traffic: 3100 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6