convert coordinates from bed file mapped to mm9(UCSC)) to GRCm38.p2 (ensembl)

[Khan, Saad M. (MU-Student)]

Hi,

I have a bed file which was mapped to mm9 genome (ucsc assembly). I want to convert this bed file coordinates to mouse ensembl version 75 (GRCm38.p2). I would be very grateful if the liftover chain file for mm9 to mouse ensembl 75 can be made available. I believe since the ucsc and ensembl use different chromosome naming conventions and different ways of naming the scaffolds as well as they have 1 based and zero based indexes ; it won't be as straightforward as just changing mm9 to mm10 and then changing the chromosome names but I may be wrong.
Kindly let me know what is the most accurate way of doing this and if possible please provide me with a chain file for the same.

regards
Saad Khan

[Luvina Guruvadoo]

Hello Saad,

Thanks for your question. Your approach is correct; first lift the file from mm9 to m10, then use a table we have (ucscToEnsembl) to convert the chromosome names. Here is a previously answered question describing this in detail:
https://groups.google.com/a/soe.ucsc.edu/d/msg/genome/GV446zcjcdg/wFPU3KRdoA8J

Note, the ucscToEnsembl file for mm10 can be found on our downloads server here:
http://hgdownload.soe.ucsc.edu/goldenPath/mm10/database/ucscToEnsembl.txt.gz

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.

Regards,

Luvina

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Luvina Guruvadoo
UCSC Genome Browser
http://genome.ucsc.edu

Saad Khan

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