Do you have 2.0 <-> 1.0 chain files?

[benbfly]

I see chain files for 1.0 <-> 1.1, but I don't see any between v1 and v2. What I need specifically are 2.0 <-> 1.0 , to analyze the T2T methylation data which is only available in v.1.0 coordinates.
Thanks!

[arangrhie]

Hello, v1.1 is identical to v2.0 for chromosomes 1-22, X. The only difference is the addition of the Y chromosome from HG002. So use the 1.0 <-> 1.1 chain.
BTW, we have the CHM13 ONT CpG methylation track for v2.0 (v1.1): https://s3-us-west-2.amazonaws.com/human-pangenomics/T2T/CHM13/assemblies/annotation/regulation/chm13v2.0_CpG_methylationFrequency.bw
We are re-calling the methylation for HG002, that will be also available soon.

[diekhans]

Hi Ben, v1.1 and v2.0 are identical, with the exception of added HG002 chrY, so those chains should work. Mark Ben Berman ***@***.***> writes:

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I see chain files for 1.0 <-> 1.1, but I don't see any between v1 and v2. What I need specifically are 2.0 <-> 1.0 , to analyze the T2T methylation data which is only available in v.1.0 coordinates. Thanks!

[benbfly]

thanks very much!

…

On Tue, Oct 11, 2022, 11:50 AM Mark Diekhans ***@***.***> wrote: Hi Ben, v1.1 and v2.0 are identical, with the exception of added HG002 chrY, so those chains should work. Mark Ben Berman ***@***.***> writes: > I see chain files for 1.0 <-> 1.1, but I don't see any between v1 and v2. What I need specifically are 2.0 <-> 1.0 , to analyze the T2T methylation data which is only available in v.1.0 coordinates. > Thanks! — Reply to this email directly, view it on GitHub <#67 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AALZ4C3QE7V2SY2X5ZYYBLLWCUS4FANCNFSM6AAAAAAQEHDGLI> . You are receiving this because you authored the thread.Message ID: ***@***.***>