Liftover file request

[Goldman, Naomi]

Hello, 

Would it be possible to provide me with a liftover file for mm10 to NOD/ShiLtJ? 

Thanks, 

Naomi Goldman 

[Brian Lee]

Dear Naomi,

Thank you for using the UCSC Genome Browser and your question about a a liftover file for mm10 to NOD/ShiLtJ.

We unfortunately have not created such a file. Please know you can find data for the hub here: http://hgdownload.soe.ucsc.edu/hubs/mouseStrains/

This data originated from alignment processes involving HAL files. You can read about these on the track description pages and also at this formats page and related publication page: 

http://genome.ucsc.edu/FAQ/FAQformat.html#format20

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3166836/

Unfortunately we are unlikely to be making a liftOver file because of this different process revolving around HAL files, which where then converted to MAF files.

There are ways that one could create chain files from the HAL file, and another option would be to download the HAL and build HAL tools and use HAL liftover. An engineer shares that building it is not for the faint of heart. You will want to refer to the above publication and FAQ link, which will in turn point to the related tools: https://github.com/ComparativeGenomicsToolkit/hal

Thank you again for your inquiry and for using the UCSC Genome Browser. 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 forum. If your question includes sensitive data, you may send it instead to genom...@soe.ucsc.edu.

All the best,

Brian Lee

UC Santa Cruz Genomics Institute

Training videos & resources: http://genome.ucsc.edu/training/index.html

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