Questions about the source of T2T-CHM13 genetic map

Question

Questions about the source of T2T-CHM13 genetic map

Opened this issue 5 months ago · 5 comments

I noticed that the T2T-CHM13 database does not list the genetic map for the T2T-CHM13 version. Is there any resource available to obtain the genetic map for the T2T-CHM13?

Answer 1 · 2024-05-31T03:21:01.000Z

Hi @lsaeric , we have a cytoband annotation. Is this what you are looking for?

Answer 2 · 2024-05-31T03:27:59.000Z

No, the genetic map I need is that can be used for calculating recombination rate.

Hi @lsaeric , we have a cytoband annotation. Is this what you are looking for?

Answer 3 · 2024-05-31T03:35:22.000Z

Sorry, then I am not aware of it..! Do you have the genetic map for hg38? I could try lift that over to CHM13 if that'll be useful.

Answer 4 · 2024-05-31T06:19:54.000Z

Sorry, then I am not aware of it..! Do you have the genetic map for hg38? I could try lift that over to CHM13 if that'll be useful.

Thank you, and you meant that there is not an available version of genetic map for T2T-CHM13 yet. Additionaly, the best approach to get the resource now is to liftover GRCh38 data to T2T-CHM13 coordinates?

Answer 5 · 2024-05-31T17:39:42.000Z

Yes I am not aware of any genetic map for T2T-CHM13.

Additionaly, the best approach to get the resource now is to liftover GRCh38 data to T2T-CHM13 coordinates?

I believe so, although it may fall apart at some corner cases.