Remove/delete a single features (sequence variants) from a feature table


(Lea Ellegaard-Jensen) #1

Hi,
I have read this previous post:

so basically I don’t know how to include/import the feature-frequency-detail.tsv into the pipeline (table.qza I guess) after removing the features(sequence variants) I don’t want to include.

Best,
Lea


(Nicholas Bokulich) #2

Hi @Uglepost,

The post you linked to is ancient (2 years old!) and the problem described there has been fixed.

If you have a particular feature you want to remove from your feature table, you can put it in a text file as shown in that post. You do not need to import this into QIIME 2. Just leave it as a text file that might look something like this:

feature-id
asv1
asv2

Call that file anything you like, but below I call it features-to-discard.tsv. Then filter out those ASVs with this command:

qiime feature-table filter-features \
 --i-table table.qza \
 --m-feature-metadata-file features-to-discard.tsv \
 --p-exclude-ids \
 --o-filtered-table filtered-table.qza

That’s all you need to do! You can carry on with filtered-table.qza and don’t need to worry about features-to-discard.tsv any longer — though you can also use it to filter your sequences file with qiime feature-table filter-seqs if that is something that you need to do.