Do I need to generate new rep-seqs after filtering?

I was able to use qiime2 and successfully denoise my data with dada2. Now I have run several of the filter methods suggested to clean up my asv table. Before I go forward with taxonomy analysis and such am I supposed to redo my rep-seqs file generated by dada2, since I probably removed some of the sequences from the table with the filtering - or does this not matter? If I do need to rerun this, I’m not sure how since the input would not be my demultiplexed sequences anymore?

Hey @bmillerlab!

It won’t really matter, you just may end up annotations for sequences you don’t really have in your feature-table anymore. This shouldn’t pose any actual problems downstream.

But! If you would like to remove these now redundant sequences, feature-table filter-seqs now accepts a feature table in the latest release: QIIME 2 2017.12!

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