Liftover files for rat genome build 8 (GRCr8)

[Eddie Yang]

Dear Genome Browser team,

I am currently working on a project that requires lifting aging-related loci from human and mouse to the updated rat genome. I came across previous conversations but only found liftover chains between different rat genome builds, so I am wondering if it is possible that you may be able to generate the liftover chains described below:

1. Human (hg19) to Rat (GRCr8/rn8)

2. Mouse (mm10) to Rat (GRCr8/rn8)

Thank you very much and I look forward to hearing from you!

Regards,

Eddie

[Matthew Speir]

Hello, Eddie. 

Thank you for your request for LiftOver files. These are now available on our download server:

• hg19 <--> GRCr8:
• https://hgdownload.soe.ucsc.edu/goldenPath/hg19/liftOver/hg19ToGCF_036323735.1.over.chain.gz
• https://hgdownload.soe.ucsc.edu/hubs/GCF/036/323/735/GCF_036323735.1/liftOver/GCF_036323735.1ToHg19.over.chain.gz
• mm10 <--> GRCr8:
• https://hgdownload.soe.ucsc.edu/goldenPath/mm10/liftOver/mm10ToGCF_036323735.1.over.chain.gz
• https://hgdownload.soe.ucsc.edu/hubs/GCF/036/323/735/GCF_036323735.1/liftOver/GCF_036323735.1ToMm10.over.chain.gz

I hope this is helpful. 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 Google Groups forum. If your question includes sensitive data, you may send it instead to genom...@soe.ucsc.edu.

---

Matthew Speir

UCSC Genome Browser, User Support

--

---
You received this message because you are subscribed to the Google Groups "UCSC Genome Browser Public Support" group.
To unsubscribe from this group and stop receiving emails from it, send an email to genome+un...@soe.ucsc.edu.
To view this discussion visit https://groups.google.com/a/soe.ucsc.edu/d/msgid/genome/e96a7fcd-8d19-419c-90b0-1607b31e9c7bn%40soe.ucsc.edu.

[Eddie Yang]

Dear Matthew,

Thanks a lot for your help! While trying to import the chain files I found that these files for some reasons could not be properly read by existing liftover functions (e.g. import.chain from rtracklayer and easyLiftOver from easyLift). 
For example, running  ch <- import.chain('./hg19ToGCF_036323735.1.over.chain') would only result in an empty chain. In comparison, previous chain files (e.g. mm10ToRn7.over.chain) can all be properly read by these functions. Therefore, I am wondering if there might be any issues with the syntax of these files that cause them unable to be read.

Sorry for more questions, and I appreciate your feedback!

Regards,

Eddie

[Clay Fischer]

Dear Eddie,

You will need to reach out to the author of rtracklayer to solve this, please CC us when you do in case we can be of assistance.

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 Google Groups forum. If your question includes sensitive data, you may send it instead to genom...@soe.ucsc.edu.

Thanks,
Clay Fischer
UCSC Genomics Institute

To view this discussion visit https://groups.google.com/a/soe.ucsc.edu/d/msgid/genome/3e5f1c1f-f926-419a-812f-79c851561e09n%40soe.ucsc.edu.