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
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
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.
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