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Those %s are both relative to the initial total # of reads. The default translated search against UniRef90 is still pretty stringent to avoid false positives. You can relax the translated search parameters yourself or have HUMAnN2 do that automatically by using UniRef50 instead of UniRef90 (to try to map more reads).Thanks,Eric
On Thu, Oct 3, 2019 at 10:11 PM Nick <nicochun...@gmail.com> wrote:
--For my analysis, I ran both nucleotide and translated protein search.Unaligned reads after nucleotide alignment: 35.8506 %...Unaligned reads after translated alignment: 31.1693 %Is the 31.1693 % of unaligned reads (ie, 31.1693 % out of 35.8506 %) or 31.1693 % of total reads?If it's the latter, it means that I only gained ~4% new alignments for a ton of compute time. Is this to be expected?
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