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How to do enrichment analysis with scipy.stats.hypergeom.sf function

I guess it is too late to answer this now, but I think you can use gseapy. Its a python module for performing enrichment ...
Eshaan IITM's user avatar
2 votes

short Read/percentage threshold for bacterium presence in metagenome

Given that you're already using kraken2, I recommend bracken: https://github.com/jenniferlu717/Bracken Bracken is a companion program to Kraken 1, KrakenUniq, or Kraken 2 While Kraken classifies ...
gringer's user avatar
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2 votes
Accepted

short Read/percentage threshold for bacterium presence in metagenome

Thats an interesting question. I do this stuff all the time and don't have a fixed cut-off. What I am certain about is 100 is marginal evidence of a species. So I personally would be reluctant to ...
M__'s user avatar
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0 votes
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Normalization in Sequence Analysis Research

Like the comments I'm not sure what the scores represent, it could be several different possibilities. Generally, we avoid recommendation if it's difficult to understand the underlying experiment. ...
M__'s user avatar
  • 12.8k

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