Request for Liftover Chain Files

[Meenakshi Bagadia]

Hello,

I need the earlier version of dolphin genome turTru1. 

Can you please provide me the chain file for LiftOver utility to convert 

1) turTru1 to hg19

2) balAcu1 to hg19 (Minke Whale)

And also the  ucscToEnsembl.txt.gz file for turTru1.

Thanks and regards

Meenakshi Bagadia

PhD student

IISER Mohali

[Meenakshi Bagadia]

HI,

Sorry, 

I wrote it wrong, I need the chain files other way round,

1) hg19 to  turTru1

2) hg19 to  balAcu1 (Minke Whale) 

Thanks 

Meenakshi

[Matthew Speir]

Hi Meenakshi,

Thank you for your LiftOver file request.

You can find the files for the hg19 to turTru1 liftOver on our preview server here:

• hg19 to turTru1: http://hgdownload-test.soe.ucsc.edu/goldenPath/hg19/liftOver/hg19ToTurTru1.over.chain.gz
  
• turTru1 to hg19: http://hgdownload-test.soe.ucsc.edu/goldenPath/turTru1/liftOver/turTru1ToHg19.over.chain.gz
  

I have also released the hg19 to balAcu1 liftOver to our public downloads server here:

• hg19 to balAcu1: http://hgdownload.soe.ucsc.edu/goldenPath/hg19/liftOver/hg19ToBalAcu1.over.chain.gz
  
• balAcu1 to hg19: http://hgdownload.soe.ucsc.edu/goldenPath/balAcu1/liftOver/balAcu1ToHg19.over.chain.gz
  

As for the "ucscToEnsembl.txt.gz" file. This table/file is not available for the turTru1 assembly. In most cases, the names in the Ensembl browser should be similar to those found in the UCSC Genome Browser. Ensembl does, however, create "gene scaffolds" for low-coverage assemblies as part of their gene prediction pipeline: http://uswest.ensembl.org/info/genome/genebuild/2x_genomes.html. We have a table, named ensemblGeneScaffold, that contains information about how these gene scaffolds overlap with the various contigs/scaffolds in the original assembly that we provide on our site. You can obtain the data for this table from the Table Browser, http://genome-test.soe.ucsc.edu/cgi-bin/hgTables.

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 Bioinformatics Group

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