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marbl / CHM13

The complete sequence of a human genome
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T2T v1.0 bed file #11

Closed tdfy closed 3 years ago

tdfy commented 3 years ago

Hello,

Do you have a bed file or coordinates for v1.0 assembly? I am filtering telomere enriched LR sequences mapped to v1.0. Thank you.

-Todd

skoren commented 3 years ago

Do you mean like the bed file for v0.9 listing which regions were patched and the locations of gaps/rDNA?

tdfy commented 3 years ago

Coordinates for telomere regions per chromosome. Example below assuming 2 Mb telomeres on either end of chromosome 1.

1 248956422 250956422 1 0 2000000

skoren commented 3 years ago

Ah OK, I was confused because there is a bed file for v0.9 but no telomere bed file for it. I ran the VGP pipeline (https://github.com/VGP/vgp-assembly/tree/master/pipeline/telomere) for telomere identification and the bed file is attached to this issue. chm13.draft_v1.0.telomere.bed.gz

tdfy commented 3 years ago

Thank you Sergey, take care

daphnar commented 3 years ago

Hi Sergey, Is there a gap/rDNA file like chm13.draft_v1.0.region.bed that is available? Thank you, Daphna