Liftover files

[YOUNG Robert]

Hi,

I’m trying to lift over two bed files, one from hg38 and the other from mm10, into a range of other species. I’ve found all but one of the chain files that I require, but there doesn’t seem to be a chain file for lifting between human hg38 and horse equcab2. There is one for lifting from mouse to horse, though.

Would you be able to produce this missing file?

Many thanks,

Rob Young

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Senior Research Associate, Taylor lab

MRC Human Genetics Unit
MRC IGMM at the University of Edinburgh
Crewe Road, Edinburgh, EH4 2XU

[YOUNG Robert]

Hi,

I emailed about a week ago asking about a lift over file between the human hg38 and horse equcab2 assemblies. 

I wonder when or if you will have time to look into this, or should I attempt to create my own file from your pairwise alignments?

Many thanks,

Rob Young

--

Senior Research Associate, Taylor lab

MRC Human Genetics Unit
MRC IGMM at the University of Edinburgh
Crewe Road, Edinburgh, EH4 2XU

Begin forwarded message:

[Matthew Speir]

Hi Rob,

Thank you for your question about obtaining a LiftOver file between Horse (equCab2) and Human (hg38). I also apologize for the delay in responding to your question.

You can now find the LiftOver chain files between these two assemblies here:
http://hgdownload.soe.ucsc.edu/goldenPath/hg38/liftOver/hg38ToEquCab2.over.chain.gz
http://hgdownload.soe.ucsc.edu/goldenPath/equCab2/liftOver/equCab2ToHg38.over.chain.gz

You can also find the pairwise alignment files between these two assemblies in a variety of formats here:
http://hgdownload.soe.ucsc.edu/goldenPath/hg38/vsEquCab2/
http://hgdownload.soe.ucsc.edu/goldenPath/equCab2/vsHg38/

If you would like to view the chain/net track for these assemblies, you can do so now here:
https://genome.ucsc.edu/cgi-bin/hgTrackUi?db=equCab2&g=chainNetHg38
https://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg38&g=placentalChainNet

Lastly, you can also now use our online LiftOver tool, https://genome.ucsc.edu/cgi-bin/hgLiftOver, to convert coordinates between hg38 and equCab2.

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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