Comments (3)
Did some samples get dropped? I think it looks at the raw counts prior to any manipulation of the OTU table.
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No samples get dropped, but the input of 'amptk filter' are the otu table and the otu fasta file generated from 'amptk cluster'. I thought that the filter command would drop otus (from otu_table) which didn't pass the number of --min_reads_otu parameter.
from amptk.
The filter is done by summing each row (OTU) and dropping those that are less than the --min_reads_otu parameter. This is done prior to any other filtering, i.e. if a mock community is used for filtering these calculations are done first. Do you have a small test case you can show me that isn't working?
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Related Issues (20)
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