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marbl / CHM13

The complete sequence of a human genome
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hg38 and chm13 1.1 liftovers? #34

Closed mvelinder closed 2 years ago

mvelinder commented 2 years ago

Are there chain files somewhere to go from: hg38 > chm13 1.1 chm13 1.1 > hg38 ?

The only way I saw to achieve this was to go from hg38 > chm13 1.0 > chm13 1.1. It'd be preferred to just go directly to 1.1

Thanks!

skoren commented 2 years ago

Unfortunately, at present no. You have to do the two-step liftover. The chain from 1.0 to 1.1 is quite simple (filling gaps) so, in my experience, it won't lose any of your features from v1.0. We should have an updated liftover once the UCSC browser is updated to 1.1 but until then you have to use both liftovers.

mvelinder commented 2 years ago

All good. Thanks @skoren ! I'll just do the two step liftover

zhoudreames commented 2 years ago

Unfortunately, at present no. You have to do the two-step liftover. The chain from 1.0 to 1.1 is quite simple (filling gaps) so, in my experience, it won't lose any of your features from v1.0. We should have an updated liftover once the UCSC browser is updated to 1.1 but until then you have to use both liftovers.

how to liftover between assemblies? we want to gain chain information from my project，thanks~