Request for Dsim2 to Dm6 chain file

[Shuai Dominique Ding]

Dear UCSC team,

I am writing to request a liftOver chain file for D. simulans to D. melanogaster coordinates conversion,

with current D. simulans Release 2 (flybase) to current D. melanogaster Release 6.

I am wondering if it is possible to also include the unassembled simulans contigs (as attached) that are not included 

in the flybase version?

[Christopher Lee]

Hello Dominique,

Thank you for your question about constructing a liftOver chain from
droSim2 to dm6. We have created this liftOver chain, and it can be
downloaded from our preview download server:
https://hgdownload-test.gi.ucsc.edu/goldenPath/dm6/liftOver/dm6ToDroSim2.over.chain.gz
https://hgdownload-test.gi.ucsc.edu/goldenPath/droSim2/liftOver/droSim2ToDm6.over.chain.gz

The droSim2 version used is the assembly available from GenBank:
ftp://ftp.ncbi.nlm.nih.gov/genomes/refseq/invertebrate/Drosophila_simulans/all_assembly_versions/GCF_000754195.2_ASM75419v2/

Please note that data on our preview download server has not yet been
reviewed by our Quality Assurance staff, and is subject to change at
any time.

There are instructions for creating your own liftOver chains available here:
http://genomewiki.ucsc.edu/index.php/DoBlastzChainNet.pl

Please let us know if you have any further questions!

Thanks,

Christopher Lee
UCSC Genomics Institute

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> Best regards,
> Dominique
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> ——————————————
> Shuai Dominique Ding
> PhD student
> Jiggins Group
> Department of Genetics,
> University of Cambridge,
> Downing Site,
> Downing Street,
> Cambridge.
> CB2 3EH
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