liftOver

[Muhammad Sohail Raza]

Hi, 

I have some questions about liftOver tool.

Actually, I am looking for lifting-over from hg38 to hg19 assembly. I have some genome-wide annotations of BED format in human hg38 assembly. But when i  looked into sample liftOver tool command , it was: 

 liftOver oldFile map.chain newFile unMapped

Here what are the additional genome files (i.e. map.chain) that i require in order to liftOver, and from where i can get them?? When we use liftOver tool, why we get unmapped regions??

Many Thanks!

sohail

************************************************************************************
Muhammad Sohail Raza

Center of Genome Variation and Biomedicine

Beijing Institute of Genomics, CAS

Beijing, China.

Phone: +8613552957083
email:   soh...@big.ac.cn

              muhammads...@live.com

[Cath Tyner]

Hi Sohail,

Thank you for using the Genome Browser and for submitting your question regarding LiftOver download files and unmapped regions.

LiftOver download files
LiftOver requires a UCSC-generated over.chain file as input. Pre-generated files are available for selected assemblies

​. Here is a direct link to the file you requested: 

hg38ToHg19.over.chain.gz

Steps for finding the file:

1. Go to

​ the UCSC Genome Browser downloads page​.

​2. ​Go to 

the​

"Dec. 2013 (hg38, GRCh38)" section

​.​

​3. C

lick the "LiftOver files" link

​ to access the list of related over.chain files.

Unmapped regions
Using the LiftOver tool, you will find unmapped regions among hg19 and hg38 since there are additions to the newer assembly, and there is not a 1-1 correspondence between the target and the query. For example, the large megabase-sized gaps that were previously used to represent centromeric regions in hg19 have been replaced by sequences from centromere models.

​ You can also view the hg38-hg19 assembly differences by turning on our "Hg19 Diff" Track under the Mapping and Sequencing section when browsing the hg38 assembly.​

Resources:

​Chain/Net ​

Wiki Discussion

Summary of hg38 release

Department of Human Genetics PowerPoint presentation "hg19 (GRCh37) vs. hg38 (GRCh38) - DTL Data" 

Thank you again for your inquiry and for using the UCSC Genome Browser. 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 togenom...@soe.ucsc.edu.

​Enjoy,​

Cath
. . .

Cath Tyner

UC Santa Cruz Genomics Institute

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