number_of_conserved_genes.Rtab

[maesaar]

1. I found that after every 100 isolates "number_of_conserved_genes.Rtab" has slight increase in conserved genes counts - could you explain?

[Example removed]

2. If new genes average count 1 then it is not plotted with Rscript?

[Examples removed]

Thanks!

[andrewjpage]

Yes. By default a core gene is defined as being present in 99% of isolates. As isolates are whole numbers, this leads to steps: 99*0.99 = ceil(98.01) = 99 (a gene is core if it is present in 99 out of 99 isolates). 100*0.99 = ceil(99) = 99 (a gene is core if it is present in 99 out of 100 isolates). 200*0.99 = ceil(198) = 198 (a gene is core if it is present in 198 out of 200 isolates). You can smooth this in R using your favourite curve fitting algorithm or can set the core definition to be 100%. Regards, Andrew

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On 12 September 2017 at 10:44, mmaesaar ***@***.***> wrote: I found that after every 100 isolates "number_of_conserved_genes.Rtab" has slight increase in conserved genes counts - could you explain? [image: number_of_conserved_genes rtab] <https://user-images.githubusercontent.com/20073096/30319223-f88c502e-97b7-11e7-9f20-11c01c845fef.png> Thanks! — You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub <#354>, or mute the thread <https://github.com/notifications/unsubscribe-auth/AABeVzCarMPMTbhSHbVZVUmSfAAMNSn9ks5shlJhgaJpZM4PUYRJ> .

[maesaar]

Thanks for the explanation!