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grenaud / gargammel

gargammel is an ancient DNA simulator
GNU General Public License v3.0
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Can I use human reference genome in the 'endo' folder? #14

Closed baif666 closed 3 years ago

baif666 commented 3 years ago

Hi,

In the tutorial, you use 'ms' to stimulate human fragments. Can I directly use the human reference genome or other modern human data in the 'endo' folder? If I don't care about the difference between ancient and present-day humans.

grenaud commented 3 years ago

yes absolutely! endo/ just means endogenous. Whatever genome you put in there will be used as endogenous. Do you care about het. sites? If so, you need 2 fasta files, 1 for each chromosome. Otherwise, it will assume the human genome is haploid.

baif666 commented 3 years ago

If I don't care about the het. site, can I put only one genome? But I found in this way, it takes more time to create aDNA fragments.

baif666 commented 3 years ago

Thanks!

grenaud commented 3 years ago

Yes absolutely, if you just put one genome, it will interpret that genome is haploid. If you do not care about heterozygous sites, this is fine :-)