LiftOver files for rat (GRCr8) and marmoset (mCalJa1.2.pat.X)

[Rong, Stephen]

Hi Genome Browser folks,

I'm currently working on a project that requires lifting functional annotations from a handful of species to updated reference genomes that are more contiguous. I was able to get from UCSC Genome Browser the liftOver chain files that I need for rhesus macaque (rheMac8ToRheMac10), mouse (mm10ToMm39), and dog (canFam3ToCanFam4). However, I still need liftOver chains for rat and marmoset, specifically:

Rat: Rnor_6.0 (GCF_000001895.5/GCA_000001895.4) to GRCr8 (GCF_036323735.1/GCA_036323735.1)

Marmoset: ASM275486v1 (GCA_002754865.1) to mCalJa1.2.pat.X (GCF_011100555.1/GCA_011100555.2)

What would be the best way to generate these liftOver chain files?

Thank you for any help you can provide!

Best regards,

Stephen Rong, PhD

Research Associate

Spivakov Lab, MRC LMS

[Luis Nassar]

Hi, Stephen.

Thanks for reaching out. We are running up these liftOver files now; they should be ready in a couple of days. We'll follow up with you then.

--

---
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/CWLP265MB4252CE1DB0DFE9E9C033F3808F212%40CWLP265MB4252.GBRP265.PROD.OUTLOOK.COM.

--

I hope this is helpful. Please include gen...@soe.ucsc.edu in any replies to ensure visibility by the team. All messages sent to that address are archived on our public forum. If your question includes sensitive information, you may send it instead to genom...@soe.ucsc.edu.

Lou Nassar
UCSC Genomics Institute

[Stephen Rong]

Hi Lou,

Any update on the liftOver files? Thank you for all of your help!

Best regards,

Stephen

[Luis Nassar]

Hi, Stephen.

The requested files are now ready. We apologize for the delay. The chain file generation failed and had to be restarted.

https://hgdownload.soe.ucsc.edu/hubs/GCA/002/754/865/GCA_002754865.1/liftOver/GCA_002754865.1ToGCA_011100555.2.over.chain.gz
https://hgdownload.soe.ucsc.edu/hubs/GCA/011/100/555/GCA_011100555.2/liftOver/GCA_011100555.2ToGCA_002754865.1.over.chain.gz
https://hgdownload.soe.ucsc.edu/goldenPath/rn6/liftOver/rn6ToGCF_036323735.1.over.chain.gz
https://hgdownload.soe.ucsc.edu/hubs/GCF/036/323/735/GCF_036323735.1/liftOver/GCF_036323735.1ToRn6.over.chain.gz

[Stephen Rong]

Hi Luis, 

Amazing, and well appreciated! Thank you!

Best,

Stephen

[Luis Nassar]

Hi, Takeshi.

We recommend the user of our API over the DAS server now (
https://genome.ucsc.edu/goldenPath/help/api.html).

For example, here is the query you wish to make on the API:

https://api.genome.ucsc.edu/getData/sequence?genome=hs1;chrom=chr1;start=100000;end=200000

How did you come across our DAS server? It does not get much attention these days.