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How can I use MIDAS to get pN/pS on a per-gene basis? #127

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JuliaMcGonigle opened this issue Mar 9, 2022 · 0 comments
Open

How can I use MIDAS to get pN/pS on a per-gene basis? #127

JuliaMcGonigle opened this issue Mar 9, 2022 · 0 comments

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@JuliaMcGonigle
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JuliaMcGonigle commented Mar 9, 2022

Per the snp_diversity.py script, documentation states: Only quantify diversity at synonymous sites (Note: use the ratio of 5/6 for pN/pS)

What does this mean? Is pN/pS calculated by running:
snp_diversity.py /path/to/snps --genomic_type per-gene --site_type 1D --locus_type CDS --out /path/to/output

and then:
snp_diversity.py /path/to/snps --genomic_type per-gene --site_type 4D --locus_type CDS --out /path/to/output

And then taking the pi value in the output for 1D/pi value in the output for 4D?

What does the ratio of 5/6 have to do with it?

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