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AdmiralenOla / Scoary

Pan-genome wide association studies
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Self created absence_presence file as input? #85

Closed maesaar closed 3 years ago

maesaar commented 3 years ago

Is it possible to use self created absence_presence data file? For example for virulence genes detected with abricate?

AdmiralenOla commented 3 years ago

Hi @mmaesaar - That is absolutely possible. Your input file has to follow the Roary gene presence/absence structure vaguely, eg the columns need to correspond to presence/absence in your input and the rows to your various genes/variants.

I strongly recommend that you reserve the first three columns in your input file for gene/variant annotation, as examplified in Roary's "Gene", "Non-unique Gene name" and "Annotation". You can have your presence/absence data starting at column 4. Make sure to alter the --start_col parameter parameter if you do this.

maesaar commented 3 years ago

Thank you @AdmiralenOla