Hello Sarah,
Thank you for using the UCSC Genome Browser and for submitting your question regarding creating your own LiftOver files for same-genome annotation lifting. We have a number of resources available:
http://genomewiki.ucsc.edu/index.php/Same_species_lift_over_construction
http://genomewiki.ucsc.edu/index.php/LiftOver_Howto
http://genomewiki.ucsc.edu/index.php/Minimal_Steps_For_LiftOver
http://genomewiki.ucsc.edu/index.php/Whole_genome_alignment_howto
Also, feel free to search our UCSC Genome Browser forum for previously answered questions related to our LiftOver tool. I recommend searching for "http://genomewiki.ucsc.edu/index.php/Same_species_lift_over_construction" in the forum to find other posts specifically related to your goal.
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.
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