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knights-lab / analysis_SHOGUN

Analysis scripts and code for reproducing the analysis for the SHOGUN paper
MIT License
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Random seeds to subsample #18

Closed FelipeMSD closed 1 year ago

FelipeMSD commented 1 year ago

Dear Benjamin,

Could you tell me if on the subsampling script you use the same or different random seeds for each depth?

Kind regards, Felipe

bhillmann commented 1 year ago

I can try, but this was done several years ago. I used different random seeds for each depth, I believe, since that is the default. https://github.com/knights-lab/analysis_SHOGUN/blob/527b1c511605608e039555fb8d238a9ba98f36c4/scripts/subsample_fasta.py#L13

Unfortunately, I don't think I saved what seeds I used, but the ability to specify them is there.

FelipeMSD commented 1 year ago

Super! Thank you very much for the response!

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From: Benjamin Hillmann @.> Sent: Friday, January 27, 2023 6:13:37 PM To: knights-lab/analysis_SHOGUN @.> Cc: Felipe Morillo Sanz Dias @.>; Author @.> Subject: Re: [knights-lab/analysis_SHOGUN] Random seeds to subsample (Issue #18)

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