Download CpG island coordinate file:

[BH Tang]

Dear Sir/Madam,

I want to download the CpG Island (>=200 or 300 bp) / CpG Shore coordinate file (HG19) from Genome Browser, could you give me any suggestions?

http://genome.ucsc.edu/cgi-bin/hgTables?db=hg19&hgta_group=regulation&hgta_track=cpgIslandExt&hgta_table=cpgIslandExt&hgta_doSchema=describe+table+schema

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chr1 Start    End    CpG island 1

...

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Secondly, could you help me download the Gene Promoter/Distal region coordinate files?

Thanks a lot.

Sincerely,

Ben

[Luvina Guruvadoo]

Hi Ben,

Thanks for your question. You may download the CpG Island table from our downloads server here: http://hgdownload.soe.ucsc.edu/downloads.html. Click on "Human" then "Annotation Database", and finally "cpgIslandExt.txt.gz". Please see the following FAQ for more information on promoters: https://genome.ucsc.edu/FAQ/FAQdownloads.html#download18.

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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Luvina Guruvadoo
UCSC Genome Bioinformatics Group

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[BH Tang]

Thanks a lot for your reply.

Could you help me figure out how to download the CpG Shore, Gene Promoter/Distal region coordinate files?

Best regards.

Sincerely,
Ben

[Steve Heitner]

Hello, Ben.

We do not have information on CpG shores.  We also do not have a file that you can download for gene promoters, but my colleague provided the link to https://genome.ucsc.edu/FAQ/FAQdownloads.html#download18 which provides instructions on how to obtain promoter sequences.

Please contact us again at gen...@soe.ucsc.edu if you have any further questions.  Questions sent to that address will be archived in a publicly-accessible forum for the benefit of other users.  If your question contains sensitive data, you may send it instead to genom...@soe.ucsc.edu.

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Steve Heitner
UCSC Genome Bioinformatics Group

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[BH Tang]

Thanks a lot Steve,

Best regards.

Sincerely,
Ben