qiime feature-table filter-features

[mamunnoz]

When checking the feature table I see that there are 5 features with a length to much shorter than expected. If these sequences where blasted they correspond with fragment of virus or clonning vector, and I am analyzing bacterias. I am trying to remove this features by qiime feature-table filter-features based in th feature-id but I can’t. Is it possible?, how can I do.

[ben (benjamin w.)]

There’s a plug-in where you can do this:

https://docs.qiime2.org/2019.7/plugins/available/quality-control/

You have to match to a database. B

[thermokarst]

Hey there @mamunnoz!

@mamunnoz

I am trying to remove this features by qiime feature-table filter-features based in th feature-id but I can’t. Is it possible?

Yep! Check out this tutorial for more details:

https://docs.qiime2.org/2019.7/tutorials/filtering/

[Luke_Thompson]

I’m having a similar issue as @mamunnoz - I would like to filter out features (sequences) that are shorter than a threshold length in bp. Is there a way to filter features from a feature table by sequence length specifically?

[thermokarst]

Hey @Luke_Thompson!

This should help you get started:

Filtering out ASVs from DADA2 based on length

Just wanted to toss out one more option for length-based filtering: qiime feature-table filter-seqs \ --i-data seqs.qza \ --m-metadata-file seqs.qza \ --p-where 'length(sequence) > 4' \ --o-filtered-data filtered-seqs.qza This works by viewing the FeatureData[Sequence] as Metadata, and then using a SQL-where clause to compute the length. The advantage here is then you don't have to export anything. This command above would keep any sequences longer than 4 nts.

[Luke_Thompson]

Thank you, @thermokarst! This looks like just what I need.