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AdmiralenOla / Scoary

Pan-genome wide association studies
GNU General Public License v3.0
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How can I explore the differences between subpopulations defined using population analysis? #100

Closed kopelol closed 2 years ago

kopelol commented 2 years ago

Hi, thank you for this attractive tool.

I'd like to explore the population specific genes using scoary.

As mentioned #64 , should I prepare trait file like this? <html xmlns:v="urn:schemas-microsoft-com:vml" xmlns:o="urn:schemas-microsoft-com:office:office" xmlns:x="urn:schemas-microsoft-com:office:excel" xmlns="http://www.w3.org/TR/REC-html40">

  | compA-B | compA-C | compB-C -- | -- | -- | -- ind1 | 1 | 0 | NA ind2 | 1 | 0 | NA .... |   |   |   ind101 | 0 | NA | 1 ind102 | 0 | NA | 1 ..... |   |   |   ind130 | NA | 1 | 0 ind131 | NA | 1 | 0

rather than <html xmlns:v="urn:schemas-microsoft-com:vml" xmlns:o="urn:schemas-microsoft-com:office:office" xmlns:x="urn:schemas-microsoft-com:office:excel" xmlns="http://www.w3.org/TR/REC-html40">

  | popA | popB | popC -- | -- | -- | -- ind1 | 1 | 0 | 0 ind2 | 1 | 0 | 0 .... |   |   |   ind101 | 0 | 1 | 0 ind102 | 0 | 1 | 0 ..... |   |   |   ind130 | 0 | 0 | 1 ind131 | 0 | 0 | 1

In addition, should I use arguments ---no_pairwise that aborts population structure correction ?

Best regards,