new genome

[肖稳]

Dear UCSC administrator,

I am very grateful to your team for providing such an important tool, liftOver, that converts genome coordinates and genome annotation files between assemblies.

But recently, I found there is no UCSC chain files for BCM_Maur_2.0 (https://www.ncbi.nlm.nih.gov/assembly/GCF_017639785.1/). If it is convenient for you, can you provide a UCSC chain file for this species (to hg19 and to mm10)?

Sure. Additionally, if you don't mind sharing, could you please let me know what parameters you used for the BLAT step? Given that human and hamster are distantly related species, setting the parameters to -tileSize=12 and -minIdentity=90 may not be appropriate.

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best!

xiaowen

The Group of Ligang Wu

Institute of Biochemistry and Cell Biology

Shanghai Institutes for Biological Sciences, CAS 

320 Yueyang Road, Shanghai

[Gerardo Perez]

Hello, Xiaowen.

Thank you for your interest in the Genome Browser.

We have made the requested liftOver chain files available on our download server:

hg19 -> GCF_017639785.1:
https://hgdownload.soe.ucsc.edu/goldenPath/hg19/liftOver/hg19ToGCF_017639785.1.over.chain.gz

GCF_017639785.1 -> hg19: https://hgdownload.soe.ucsc.edu/hubs/GCF/017/639/785/GCF_017639785.1/liftOver/GCF_017639785.1ToHg19.over.chain.gz

mm10 -> GCF_017639785.1:
https://hgdownload.soe.ucsc.edu/goldenPath/mm10/liftOver/mm10ToGCF_017639785.1.over.chain.gz

GCF_017639785.1 -> mm10:
https://hgdownload.soe.ucsc.edu/hubs/GCF/017/639/785/GCF_017639785.1/liftOver/GCF_017639785.1ToMm10.over.chain.gz

Regarding the parameters used, we used the doBlastzChainNet.pl script with the lastz parameters since it tends to do better for human-rodent distances or greater. We offer some example lastz parameters on the following wiki pages:
http://genomewiki.ucsc.edu/index.php/DoBlastzChainNet.pl#lastz_parameter_file
http://genomewiki.ucsc.edu/index.php/Lastz_DEF_file_parameters

We can point you towards our makedocs for GCF_017639785.1 to hg19 and mm10 lastz runs. Keep in mind these are more so made for internal replication. You can find the makedocs below on git:

hg19: https://github.com/ucscGenomeBrowser/kent/blob/master/src/hg/makeDb/doc/asmHubs/lastzRuns.txt#L2298

mm10: https://github.com/ucscGenomeBrowser/kent/blob/master/src/hg/makeDb/doc/asmHubs/lastzRuns.txt#L2382

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.

Gerardo Perez
UCSC Genomics Institute

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