Outputting a format for COLONY

[Ryan]

Dear all,

I have rad-seq data of many samples of bumblebee and I'm using Stacks to help analyse it. However, one step I want to do is to identify siblings, so I can just use one bee sample per colony in the analysis. The software I was recommended and is commonly used to do this is COLONY, but you have to make its custom input file. I used populations to get the Structure file format, as this was similar to COLONY, but I've found it's not similar enough.

Does anyone know a better approach to use Stacks to produce the sample ID and genotype of each sample in the format needed for COLONY? Or any other way I can do this?

Thank you for reading this.

All the best,

Ryan

[Ingrid Spies]

Hi Ryan

I've used Colony but it can only take a limited number of SNPs. Setting up the files was a pain - I can send you examples if you like, but later I tried apparent, an R package https://cran.r-project.org/src/contrib/Archive/apparent/ which could use all my data and I liked better. I see that it seems to have been archived though....

Ingrid

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[Brenna Levine]

Hi Ryan,

For pedigree reconstruction, you might want to try the R package Sequoia by Jisca Huisman. It's designed for SNPs and you can use a plink file output from Stacks as the input. 

Brenna 

To view this discussion on the web visit https://groups.google.com/d/msgid/stacks-users/CAGz-WwE3SvCXzxhdU%3D%2Bh6QgmY7MXBiacPd%2BMModTjLBxenMcug%40mail.gmail.com.

[Ryan]

Thank you for the advice Ingrid!

All the best,

Ryan

On Wednesday, 25 March 2020 13:13:40 UTC, Ingrid Spies wrote:

Hi Ryan

I've used Colony but it can only take a limited number of SNPs. Setting up the files was a pain - I can send you examples if you like, but later I tried apparent, an R package https://cran.r-project.org/src/contrib/Archive/apparent/ which could use all my data and I liked better. I see that it seems to have been archived though....

Ingrid

On Wed, Mar 25, 2020 at 5:48 AM Ryan <ryanel...@gmail.com> wrote:

Dear all,

I have rad-seq data of many samples of bumblebee and I'm using Stacks to help analyse it. However, one step I want to do is to identify siblings, so I can just use one bee sample per colony in the analysis. The software I was recommended and is commonly used to do this is COLONY, but you have to make its custom input file. I used populations to get the Structure file format, as this was similar to COLONY, but I've found it's not similar enough.

Does anyone know a better approach to use Stacks to produce the sample ID and genotype of each sample in the format needed for COLONY? Or any other way I can do this?

Thank you for reading this.

All the best,

Ryan

--
Stacks website: http://catchenlab.life.illinois.edu/stacks/
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[Ryan]

Hi Brenna,

Thank you for for reply and this advice!

All the best,

Ryan

On Wednesday, 25 March 2020 14:53:59 UTC, Brenna Levine wrote:

Hi Ryan,

For pedigree reconstruction, you might want to try the R package Sequoia by Jisca Huisman. It's designed for SNPs and you can use a plink file output from Stacks as the input. 

Brenna 

On Wed, Mar 25, 2020, 8:13 AM Ingrid Spies <ingrid...@gmail.com> wrote:

Hi Ryan

I've used Colony but it can only take a limited number of SNPs. Setting up the files was a pain - I can send you examples if you like, but later I tried apparent, an R package https://cran.r-project.org/src/contrib/Archive/apparent/ which could use all my data and I liked better. I see that it seems to have been archived though....

Ingrid

On Wed, Mar 25, 2020 at 5:48 AM Ryan <ryanel...@gmail.com> wrote:

Dear all,

I have rad-seq data of many samples of bumblebee and I'm using Stacks to help analyse it. However, one step I want to do is to identify siblings, so I can just use one bee sample per colony in the analysis. The software I was recommended and is commonly used to do this is COLONY, but you have to make its custom input file. I used populations to get the Structure file format, as this was similar to COLONY, but I've found it's not similar enough.

Does anyone know a better approach to use Stacks to produce the sample ID and genotype of each sample in the format needed for COLONY? Or any other way I can do this?

Thank you for reading this.

All the best,

Ryan

--
Stacks website: http://catchenlab.life.illinois.edu/stacks/
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[Thierry Gosselin]

Try this Ryan

https://thierrygosselin.github.io/radiator/reference/write_colony.html

Cheers

Thierry

[Samantha Ockhuis]

Dear Ingrid,

I would like to use COLONY for pedigree reconstruction. I see from your response that you have used this before but found that setting up the files was difficult. I wanted to know, how did you convert your files for colony format? There is an R package genepopedit where you can convert your genepop file into COLONY format, however I keep on getting errors trying this conversion. How did you convert your files for COLONY format?

Hope to hear from you soon!

Kind Regards,

Samantha

[Karina Soares]

Hi  Samantha!

Did you manage to convert the file? What did you use?

Cheers,

Karina