how to obtain chain information from any two assemblies(liftover)

Question

how to obtain chain information from any two assemblies(liftover)

zhoudreames opened this issue 2 years ago · 3 comments

zhoudreames commented 2 years ago

I want to use my assembled genome to liftover reference genome, how to do it? thanks ~

Answer 1 · 2022-03-14T16:18:24.000Z

liftover files for V1.1 are in
http://t2t.gi.ucsc.edu/chm13/hub/t2t-chm13-v1.1/downloads/

V2.0 is not available yet

Answer 2 · 2022-03-15T00:39:25.000Z

liftover files for V1.1 are in http://t2t.gi.ucsc.edu/chm13/hub/t2t-chm13-v1.1/downloads/

V2.0 is not available yet

thanks for your reply, can I make the leftover files by myself? i want to obtain the chain files from my assembled genome. how to do it ? thanks again~

Answer 3 · 2022-03-15T00:50:57.000Z

This question doesn't seem specific/relevant to CHM13. Are you're just interested in how to build a new chain file? This wiki has some information: http://genomewiki.ucsc.edu/index.php/LiftOver_Howto and there's more guides if you just google for how to build chain files.