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?
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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