make a genitic map from zero

[Luigi Faino]

Dear,

I'm new to R/qtl and i need some help. I need to build a new genetic map from scratch meaning that i have an F2 population and marker genotypes.

I see that R/qtl can be used but i can not really understand how.  From what i see, I need to start from a geno file and a pheno file and in the geno file i need to have chromosome and position of each marker. However, I do not have this information. 

which king of file do i need to have to make a linkage map starting only from the marker information?

thanks

L

[Karl Broman]

Assign arbitrary values. For example, put "un" for the chromosome for all markers, and give them positions 1, 2, 3, ...

karl

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[Luigi Faino]

ok i did it and it works.

however i have another problem. I have many linkage groups and i would like to keep only the largest 11. do you have any idea on how to do it?

L

[Karl Broman]

It’s hard to say without knowing more about the situation.

There is a tutorial on genetic map construction with R/qtl: https://rqtl.org/tutorials/geneticmaps.pdf

karl

[Luigi Faino]

this is an example of my data:

n.mar length ave.spacing max.spacing 1 355 3540 10 10 2 351 3500 10 10 3 344 3430 10 10 4 340 3390 10 10 5 261 2600 10 10 6 243 2420 10 10 7 207 2060 10 10 8 174 1730 10 10 9 173 1720 10 10 10 152 1510 10 10 11 96 950 10 10 12 22 210 10 10 13 19 180 10 10 14 11 100 10 10 15 10 90 10 10 16 10 90 10 10 17 10 90 10 10 18 9 80 10 10 19 8 70 10 10 20 8 70 10 10 21 8 70 10 10 22 7 60 10 10 23 7 60 10 10 24 7 60 10 10 25 6 50 10 10 26 6 50 10 10

I want to keep only the 11 top linkage groups

L

[Karl Broman]

You can use drop.markers to remove the other markers from the dataset, or movemarker to move them to some other “unlinked” linkage group.

karl

[Luigi Faino]

Dear

 what do you think about this map? can you advice any adjustments or modification?

L

[Samuel Wang]

Dear L:

What methods were used to generate the genotype data?

If the genotype data were generated from the next-generation sequencing method, I would suggest removing the genotype as missing with a genotype quality less than 20, and the marker missing rate should less than 0.25.

The genotype would become easier to build the reasonable linkage map.

Samuel

On Dec 28, 2024, at 06:30, Luigi Faino <luigi...@gmail.com> wrote:

Dear

 what do you think about this map? can you advice any adjustments or modification?

L<RplotMAP.jpeg>

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