Advice to filter in populations

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Sergio Taboada

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Sep 6, 2022, 7:33:43 AM9/6/22
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Hi all,

We might need some help from you for some analyses we are trying to conduct on a study of sex-determination in sponges using ddRADsex. It might be quite a simple question but we definitively have not found a way to solve it.

We have two populations (males vs females) and we need the SNPs only appearing in one of them (just males or just females). We tried with '-p 1' and '-r 1.0' to select individuals at least in one of the populations and present in 100% of the individuals, but this does not provide us with the SNPs we need, since SNPs present in one population might also be present in a few individuals from the other population.

The ideal would be having a function filtering individuals from just 1 population, but it does not occur in Stacks.

Any thoughts?

Thanks in advance and sorry for the silly question,

Sergi.

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Sergi Taboada
Profesor Ayudante Doctor
Universidad Complutense de Madrid
Facultad de Ciencias Biológicas
Departamento de Biodiversidad, Ecología y Evolución
C/ José Antonio Novais, 12. 28040 Madrid
Planta 10, Despacho 18
Telf. +34 91 394 (4664)

-----------------------------------------------------------------------------

Sergi Taboada

The Natural History Museum of London

Life Sciences Dept., Invertebrates Division
DC1, 6th floor
Office 605

Cromwell Road, SW7 5BD, London (UK)
Telephone: +44 (0) 20 7492 5433

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Edgar Caballero

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Sep 6, 2022, 8:45:50 AM9/6/22
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Hi Sergi, good morning 
I am new to using Stacks, but I think I can help you with that. You may want to modify your popmap file and just use a single population (it could be either male or female) and adjust the parameters to get all the snps from that population, this will limit the samples that would be analysed. This is my suggestion but if anyone else come up with other ideas that's awesome.

Sergi I am from Panama if you wish you can write in spanish,

if you have questions or doubts I would be happy to help,
best,
Edgar

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Catchen, Julian

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Sep 6, 2022, 2:17:32 PM9/6/22
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Hi Sergi,

 

Code your individuals as male or female in the population map. Then execute populations and look for private alleles (marked in the populations.sumstats output file). These will be alleles occurring only in one population or the other, but not both.

 

Best,

 

julian

Sergio Taboada

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Sep 7, 2022, 1:26:06 AM9/7/22
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Thanks for the advice, Julian.
Best,

Sergi.

-----------------------------------------------------------------------------
Sergi Taboada
Profesor Ayudante Doctor
Universidad Complutense de Madrid
Facultad de Ciencias Biológicas
Departamento de Biodiversidad, Ecología y Evolución
C/ José Antonio Novais, 12. 28040 Madrid
Planta 10, Despacho 18
Telf. +34 91 394 (4664)

-----------------------------------------------------------------------------

Sergi Taboada

The Natural History Museum of London

Life Sciences Dept., Invertebrates Division
DC1, 6th floor
Office 605

Cromwell Road, SW7 5BD, London (UK)
Telephone: +44 (0) 20 7492 5433

------------------------------------------------------

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Stacks website: http://catchenlab.life.illinois.edu/stacks/
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