Please help me with liftover

[Jian Wang]

Dear Sir/Madam

I want to genome coordinates between Rainbow Trout and zebrafish. But I can not find liftover file on UCSC website. Would you try to help me with that?

Thank you

Jian

[Matthew Speir]

Hi Jian,

Thank you for your question about liftOver files to convert coordinates between rainbow trout and zebrafish. Unfortunately, we don't host a rainbow trout genome browser, which means that we don't have any liftOver files for this conversion. However, you can create your own liftOver file to convert coordinates between the rainbow trout and zebrafish. Please see the instructions on the following pages for more information on creating your own liftOver files:

• http://genomewiki.ucsc.edu/index.php/Minimal_Steps_For_LiftOver
• http://genomewiki.ucsc.edu/index.php/LiftOver_Howto

You can find many of the utilities (i.e. blat, liftUp, axtChain, etc.) mentioned on those pages on our download server at http://hgdownload.soe.ucsc.edu/admin/exe under the folder for your particular system. You can also find the zebrafish (danRer7) 2bit file that you will need on our download server here: http://hgdownload.soe.ucsc.edu/goldenPath/danRer7/bigZips/danRer7.2bit.

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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