Liftover for X. laevis

[Ian Quigley]

Hey, imagine the Xenopus genome consortium has been lobbying you guys to support the X. laevis genome (v9.1, downloadable here). I get that these things take time, but could I trouble you for a liftover chain file so I can compare frog to mouse/human coordinates?

Many thanks for any and all assistance,

i

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Ian Quigley, Ph.D
Research Associate
Molecular Neurobiology Lab - Kintner
Salk Institute for Biological Studies
10010 North Torrey Pines Road
La Jolla, CA 92037

(858)453-4100 ext. 1393
iqui...@salk.edu

[Brian Lee]

Dear Ian,

Thank you for using the UCSC Genome Browser and your question about the X. laevis genome. We do no currently have a X. laevis genome release planned.

The currently released Xenopus data is for the Nov. 2009 Xenopus (Silurana) tropicalis (western clawed frog) assembly (GCA_000004195.1) and can be found here, http://genome.ucsc.edu/cgi-bin/hgGateway?db=xenTro3, with related human and mouse liftover files available here: http://hgdownload.soe.ucsc.edu/goldenPath/xenTro3/

You may be interested to learn we have an assembly release planned for xenTro7 (GenBank accession ID: GCA_000004195.2) once it passes a final QA quality check. Unfortunately it is not clear when the release will happen, but it is currently available on our test server, where data is subject to change: http://genome-test.soe.ucsc.edu/cgi-bin/hgGateway?db=xenTro7

For the xeonTro7 release, there are also already some human (hg19 and hg38) and nanPar1 (Tibetan Frog) liftOver files available from our test server: http://hgdownload-test.soe.ucsc.edu/goldenPath/xenTro7/

Specifically for X. laevis, you may wish to consider building an Assembly hub. Assembly hubs allow independent individuals to host genome data that can be browsed over the internet on the Browser. Please see these resources for more information: 

http://genomewiki.ucsc.edu/index.php/Assembly_Hubs

http://genome.ucsc.edu/goldenPath/help/hubQuickStartAssembly.html

You can also follow the independent wikisteps here to create liftOver files indepednently: http://genomewiki.ucsc.edu/index.php/LiftOver_Howto

Thank you again for your inquiry and 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.

All the best,

Brian Lee

UCSC Genomics Institute

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[Ian Quigley]

Thanks for getting back to me, I'll try to make my own.

Is there anyone over there to lobby to include X. laevis? There are currently >27,000 X. laevis papers indexed in Pubmed, as compared to, say, 76 for elephant shark. We've already mapped a bunch of histone mods with chipseq (H3K4me3, H3K27ac, H3K4me2, H3K27me3), plus transcription factors/DNA-binding proteins (foxj1, foxn4, myb, e2f4, rfx2, rad21) and done HiC across multiple tissue types and timepoints, plus >2B RNAseq reads (>100 libraries), and that's just my lab! Moreover, the genome paper's about to be submitted. UCSC support could really make this system hum, we'd love to be on board.

Thanks for any and all sympathies,

i

[Brian Lee]

Dear Ian,

Thank you for using the UCSC Genome Browser and your question about including X. laevis.

One of our engineers took a look and discovered that this assembly is not available at GenBank and we currently focus only on assemblies that are available through GenBank. One of our engineers strongly suggests you prompt the assemblers of this genome to get it submitted to the NCBI assembly system: http://www.ncbi.nlm.nih.gov/assembly/

Once the assembly is available there it will have an increased chance of being used by NCBI, Ensembl, and UCSC. Also the chance will increase that other individuals in the wider bioinformatics community may create an assembly hub through automated processes once it is available through GenBank.

Thank you again for your inquiry and 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.

All the best,

Brian Lee

UCSC Genomics Institute