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alachins / raisd

RAiSD: software to detect positive selection based on multiple signatures of a selective sweep and SNP vectors
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Results interpretation #36

Open glaudelrio opened 2 years ago

glaudelrio commented 2 years ago

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.

image

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

Thank you so much!

glaudelrio commented 2 years ago

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 commented 2 years ago

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.

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 https://github.com/alachins/raisd/issues/36#issuecomment-1124505971, or unsubscribe https://github.com/notifications/unsubscribe-auth/AALKWCRGVGPBJPBSGBQ4ELDVJR7DPANCNFSM5VW4NW7A . You are receiving this because you are subscribed to this thread.Message ID: @.***>

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glaudelrio commented 2 years ago

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 commented 2 years ago

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

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 https://github.com/alachins/raisd/issues/36#issuecomment-1134769901, or unsubscribe https://github.com/notifications/unsubscribe-auth/AALKWCWUKBWLSZFLXN6QJ4LVLOKZZANCNFSM5VW4NW7A . You are receiving this because you commented.Message ID: @.***>

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glaudelrio commented 2 years ago

Thank you very much!

glaudelrio commented 2 years ago

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 commented 2 years ago

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 commented 2 years ago

Awesome! Thank you so much!

c-hacke commented 1 year ago

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 commented 1 year ago

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

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 https://github.com/alachins/raisd/issues/36#issuecomment-1288965629, or unsubscribe https://github.com/notifications/unsubscribe-auth/AALKWCVVY7YPHKQJYM25O4TWEZ6XPANCNFSM5VW4NW7A . You are receiving this because you commented.Message ID: @.***>

-- Nikolaos Alachiotis