Filtering fasta sequences file based on a list of OTUs

[Ina (Timling)]

Hello,
I have a list of OTUs ( Ids) that I want to select from a larger file with fasta sequences. How can I do this in QIIME2?

[thermokarst]

Hey there @Ina!

@Ina

How can I do this in QIIME2?

First, import your seqs as FeatureData[Sequence]. Then, use ID-based filtering to select the features you are interested in (the command in the tutorial is for filtering feature tables, but the ideas are the same, use feature-table filter-seqs instead).

Keep us posted! :qiime2:

[Ina (Timling)]

Hello Matthew,
Thank you so much for your help. It worked!
Below are the commands I used. I hope they will be of use for others.

import data ( fasta sequences ‘query.fa’) and output as artifact (‘query_sequences.qza’)

qiime tools import
--input-path query.fa
--output-path query_sequences.qza
--type FeatureData[Sequence]

Filtering seq (‘query_sequences.qza’) based on a list of OTU names in tab-delimited file( ‘NAAT_EAT_OTUlist.txt’) and outputting (into ‘NAAT_EAT_3431OTUs.qza’)

qiime feature-table filter-seqs
--i-data query_sequences.qza
--m-metadata-file NAAT_EAT_OTUlist.txt
--o-filtered-data NAAT_EAT_3431OTUs.qza