How to create a map.chain file?

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Sarah Djebali

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Jan 13, 2016, 10:15:17 AM1/13/16
to gen...@soe.ucsc.edu, Kévin Muret
Hi all,

I have two assemblies from the same genome and I would like to lift some annotations from the old to the new assemblies.

I would like to use liftOver for this but I do not have any map.chain file, is it possible for me to create my own map.chain file? do you have a tool for this?

Thanks,
Sarah

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Sarah Djebali Quelen - PhD
INRA GenPhySE, ch. de Borderouge
31326 Castanet-Tolosan, France
Tel. +33 5 61 28 51 22
sarah.djebali-quelen at toulouse dot inra dot fr

Cath Tyner

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Jan 13, 2016, 6:21:52 PM1/13/16
to Sarah Djebali, UCSC Genome Browser Public Help Forum, Kévin Muret

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.

​Enjoy,​

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