Results interpretation

[glaudelrio]

Hi I am facing some issues interpreting the results... how do I know which parts of the genome are sweeps?

Here is just one of the plots generated with part of my data. I would love some input.

Also, how did you produce the figure 6a of your manuscript?

Thank you so much!

[glaudelrio]

I am dealing with a hybrid zone between two closely related species. Do you suggest running RAiSD with only one of the populations?
Thank you for any help!
Best wishes

[alachins]

Hello! In the absence of neutral simulated data to determine the cutoff threshold, you can assume a cutoff threshold at the top x% of your scores for the final μ scores (bottom right plot) and the regions with scores above this threshold are candidate sweep regions. In your results, note that μ_sfs is not informative which means that you have no singletons in your data. Did you filter them out? You can use the -c flag to include doubletons etc. We used the Omiccircos R application to create figure 6a. Best regards, Nikos A.

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On Thu, May 12, 2022 at 6:02 AM Glaucia Del-Rio ***@***.***> wrote: I am dealing with a hybrid zone between two closely related species. Do you suggest running RAiSD with only one of the populations? Thank you for any help! Best wishes — Reply to this email directly, view it on GitHub <#36 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AALKWCRGVGPBJPBSGBQ4ELDVJR7DPANCNFSM5VW4NW7A> . You are receiving this because you are subscribed to this thread.Message ID: ***@***.***>

-- Nikolaos Alachiotis

[glaudelrio]

Quick, question! The top values in the mu plot could indicate selective sweeps, so do the valleys (significantly lower values than average) have any meaning?
Thank you so much!

[alachins]

By singletons I meant polymorphic sites with just one mutation. The low-score regions correspond to neutral regions.

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On Mon, May 23, 2022 at 4:45 PM Glaucia Del-Rio ***@***.***> wrote: Quick, question! The top values in the mu plot could indicate selective sweeps, so do the valleys (significantly lower values than average) have any meaning? Thank you so much! — Reply to this email directly, view it on GitHub <#36 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AALKWCWUKBWLSZFLXN6QJ4LVLOKZZANCNFSM5VW4NW7A> . You are receiving this because you commented.Message ID: ***@***.***>

-- Nikolaos Alachiotis

[glaudelrio]

Thank you very much!

[glaudelrio]

Thank you so much for all the help! I have 3 questions:

1. are the results comparable across scaffolds?
2. are the results comparable across populations?
3. It seems that chromosomal inversions show up as mu peaks? Is this an artifact?
   Thank you!!!!

[alachins]

Yes, the results are comparable across scaffolds and populations.
It can happen that chromosomal inversions inflate the μ values, which could be the case if there are not many mutations for instance. This will increase the μ_var factor.

[glaudelrio]

Awesome! Thank you so much!

[c-hacke]

Hello,
If I decide to create neutral simulated data for the cutoff threshold are there any tools you would recommend using, or general recommendations for the process to ensure good results when calculating the threshold?

[alachins]

ms and msprime are two of the tools that you can use.

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On Mon, Oct 24, 2022 at 2:32 PM c-hacke ***@***.***> wrote: Hello, If I decide to create neutral simulated data for the cutoff threshold are there any tools you would recommend using, or general recommendations for the process to ensure good results when calculating the threshold? — Reply to this email directly, view it on GitHub <#36 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AALKWCVVY7YPHKQJYM25O4TWEZ6XPANCNFSM5VW4NW7A> . You are receiving this because you commented.Message ID: ***@***.***>

-- Nikolaos Alachiotis