about RepeatMasker

[Bogdan Tanasa]

Dear all,

please could you advise about the coordinates repStart, repEnd and repLeft in the output of RepeatMasker, and about the Reference Sequences of Retrotransposons that the program uses. thank you,

-- bogdan

[Steve Heitner]

Hello, Bogdan.

A very similar question was asked recently.  Please see https://groups.google.com/a/soe.ucsc.edu/d/msg/genome/IEP_aZjQp_s/-XB_nPwWcEMJ.  You can also view the schema of the RepeatMasker track by viewing the track description page (http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg19&g=rmsk) and clicking the “View table schema” link.

I believe your question about the reference sequences of transposons that the program uses would be best directed to the folks at RepeatMasker.

Please contact us again at gen...@soe.ucsc.edu if you have any further questions.  All messages sent to that address are archived on a publicly-accessible Google Groups forum.  If your question includes 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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[Bogdan Tanasa]

Hi Steve,

thank you for your reply. If I may add one more question, this is about the the data from ENCODE or RoadMap Epigenomics :

are the latest tracks from ENCODE or Roadmap Epigenomics already available in UCSC genome browser ? thanks, and happy weekend,

bogdan

[Brian Lee]

Dear Bogdan,

Thank you for your question about the latest tracks from ENCODE or Roadmap Epigenomics. For the latest information from both these sources you should contact them directly.

At UCSC, only ENCODE data from 2003 to 2012, capturing the pilot project and previous “ENCODE2” phase, are accessible currently. See the top of our ENCODE page, http://genome.ucsc.edu/ENCODE/, for more information.

The new ENCODE portal, https://www.encodeproject.org, includes any new data produced from 2013 to present day, as well as all publicly available ENCODE data. For ENCODE data questions, please contact the ENCODE portal at encod...@lists.stanford.edu

At UCSC, for the Roadmap Epigenomics project, we feature two Public Hubs, http://genome.ucsc.edu/cgi-bin/hgHubConnect, externally maintained and updated by the Roadmap Project. You can find one hub for their Complete Collection and a second Integrative Analysis Hub: http://genome.ucsc.edu/cgi-bin/hgTracks?db=hg19&hubUrl=http://vizhub.wustl.edu/VizHub/RoadmapIntegrative.txt

For all Roadmap Epiginomics data questions, please contact their website, http://www.roadmapepigenomics.org/

In summary, you should send questions directly to ENCODE or the Roadmap Epigenomics Group with any questions about their very latest information. If you have any further UCSC 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 Genome Bioinformatics Group

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