Fwd: [cbseweb] mouse tracks

[Branwyn Wagman]

A question from the cbse web site that should have gone to the browser group...

-------- Forwarded Message --------

Subject:	[cbseweb] mouse tracks
Date:	Fri, 13 Feb 2015 20:43:16 -0500
From:	Miano, Joseph <joseph...@URMC.Rochester.edu>
Reply-To:	joseph...@urmc.rochester.edu
To:	'cbs...@soe.ucsc.edu' <cbs...@soe.ucsc.edu>

Hi,

Could you tell me when (or how) the new mouse ENCODE tracks may be accessed on the UCSC Browser?

Thanks!
Joe

 

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Branwyn Stewart Wagman
Director of Development & Communications
UC Santa Cruz Genomics Institute
Center for Biomolecular Science and Engineering (CBSE)
California Institute for Quantitative Biosciences (QB3)

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[Brian Lee]

Dear Joe,

Thank you for using the UCSC Genome Browser and your question about accessing new ENCODE tracks on the UCSC Genome Browser. ENCODE Data up until 2012 can be found at http://genome.ucsc.edu/ENCODE/, where there is a Mouse Experiment Matrix visualizing assays against cell types: http://genome.ucsc.edu/ENCODE/dataMatrix/encodeDataMatrixMouse.html

Currently, for ENCODE data generated after 2012, you will want to visit the ENCODE Portal, https://www.encodeproject.org/help/getting-started, and send any questions to their list at encod...@lists.stanford.edu. In the future, when the current stage of ENCODE has generated uniformly processed data, there will likely be clustered data tracks in the UCSC Genome Browser of the ENCODE's finalized integrated data.

Please see the ENCODE portal's getting started page for more information, but here is a quick summary of the process of viewing new 2014 mm9 data from the site. By clicking the "Data" top menu and "Assays", you can then click the "mm9" facet for visualizable files on the mm9 assembly, and then go to "Date released" and select all 2014 dates. The following link performs the above steps:

https://www.encodeproject.org/search/?type=experiment&month_released=June%2C+2014&month_released=March%2C+2014&assembly=mm9&month_released=February%2C+2014

You can then click the "Visualize" link and a Browser session will appear with a hub displaying a few of the matching assays. You can click the UCSC Browser "configure" button and then scroll right and select "show all" for the ENCODE Portal generated "Hub (search)" and then click "submit" to see all the files. Please note also that there are many recent fastq files that this above search will not collect, as the above was limited to searching visualizable files (by clicking the mm9 facet). Again, the ENCODE portal is maintained externally from UCSC. For further ENCODE data questions, please contact encod...@lists.stanford.edu.

Thank you again for your inquiry and using the UCSC Genome Browser. 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