where to get reference taxonomy for training custom classifier?

[saeedmn (Saeed)]

Dear colleagues, I'm using qiime2 to analyze my paired-end reads of rbcl gene to find out the floral composition of some samples. I need to make database for rbcl gene. I made my ref-seqs.qza using following commands:

qiime tools import --input-path rbcl_upper.fasta --output-path rbcl.qza --type 'FeatureData[Sequence]'
qiime feature-classifier extract-reads --i-sequences rbcl.qza --p-f-primer TGGCAGCATTYCGAGTAACTC --p-r-primer GTAAAATCAAGTCCACCRCG --p-trunc-len 400 --o-reads ref-seqs.qza

Now I need to make 'ref-taxonomy.qza' but I don't know how to generate "taxonomy.txt" file. Please help me to overcome this problem

Thanks in advance

[SoilRotifer (Mike Robeson)]

Hi @saeedmn,

This sounds like a job for RESCRIPt! Specifically, check out:

Using RESCRIPt to compile sequence databases and taxonomy classifiers from NCBI Genbank

This tutorial will describe how to create custom reference databases from NCBI Genbank using RESCRIPt. Read more about RESCRIPt here: https://forum.qiime2.org/t/processing-filtering-and-evaluating-reference-sequence-data-with-rescript/15494/7 If using NCBI Genbank data, please be aware of the NCBI disclaimer and copyright notice. Citation: If you use RESCRIPt or any RESCRIPt-processed data in your research, please cite the following pre-print: Michael S Robeson II, Devon R O'Rourke, Benjami…

-Cheers!

[saeedmn (Saeed)]

Thank you for your reply. Sounds great!