using q2-fragment insertion to filter sequences

[lizgehret]

Hi @anna-schrecengost,

@anna-schrecengost

Do you know if there is a way in QIIME to filter ASV tables by a list of feature IDs that I copy from the tree?

I'm not sure if this is exactly what you're looking for, but this forum post does go over filtering on specific ASVs in QIIME 2 - which may be useful if you go the QIIME 2 route!

@anna-schrecengost

Or, if I prune the tree in a different program, and obtain a tree with only my target ASVs (as well as the reference), I could use that tree with qiime fragment-insertion filter-features to obtain an ASV table with only target sequences, and then re-run qiime fragment-insertion sepp with that ASV table --- does that seem reasonable?

This seems reasonable to me, so if you don't have any luck with the suggestion in that separate forum post above, I would recommend taking this route!

Cheers,
Liz