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sjdlabgroup / SAHMI

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"cell.lines.txt" or "Table S4" don't include some taxas #7

Open ZhangMH2000 opened 1 year ago

ZhangMH2000 commented 1 year ago

Dear author: Thank you for developping this wonderful tools. When I'm applying it to my data, there are some taxas that are not included in "cell.lines.txt" or "Table S4" when I'm doing decontamination. The principle of decontamination is to consider taxa with a proportion lower than 95% or 99% of CLQT in the sample as contaminated, while those above the threshold are considered true positive. In that case, can I assume that the actual proportion of taxa not present in CLQT is 0%, and then consider that the taxa present in the sample is truly positive? Sincerely looking forward to your reply, thank you!

StackChan commented 5 months ago

I think you should for sure consider that the taxa present in the sample is truly positive. And I encounter many such cases while I use it. blabla