Question about Liftover

[Hyunho Kim]

Dear UCSC genome browser administer,

This is Hyunho Kim of Genome Research Foundation in Korea.

I have some question about Liftover.

We will conduct to do Liftover about Hg38 to CHM1 whole genome alignment data.

This is my question. 

1. What is recommend of the lastz and blat for Liftover?

2. Can you tell me the using Liftover option(BLAT or Lastz)?

We look forward to your answer.

Thanks.

-Hyunho-

 

[Luvina Guruvadoo]

Hello Hyunho,

Thank you for your question. We recommend using BLAT for same species liftOver and the lastz pipeline for more distant species. Please see the following wiki page for more information:
http://genomewiki.ucsc.edu/index.php/Same_species_lift_over_construction. Hopefully, this will help you decide which method to use.

If you have any further questions, please reply to gen...@soe.ucsc.edu. All messages sent to that address are archived on a publicly-accessible forum. If your question includes sensitive data, you may send it instead to genom...@soe.ucsc.edu.

Regards,

Luvina

--

Luvina Guruvadoo
UCSC Genome Browser
http://genome.ucsc.edu

--

--

Luvina Guruvadoo
UCSC Genome Browser
http://genome.ucsc.edu