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marbl / CHM13

The complete sequence of a human genome
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Do you have 2.0 <-> 1.0 chain files? #67

Closed benbfly closed 1 year ago

benbfly commented 1 year ago

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 commented 1 year ago

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 commented 1 year ago

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!

benbfly commented 1 year ago

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!

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