Question: How to map taxonomy to OTUs
0
gravatar for xioli2013
9 months ago by
xioli20130
xioli20130 wrote:

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

taxonomy table trnl otu • 352 views
ADD COMMENTlink modified 9 months ago • written 9 months ago by xioli20130

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 REPLYlink written 9 months ago by Trombone Engineer0

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

ADD REPLYlink written 9 months ago by xioli20130
1
gravatar for xioli2013
9 months ago by
xioli20130
xioli20130 wrote:

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 COMMENTlink written 9 months ago by xioli20130
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