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2012-05-18 DCC Progress

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July 2012 Data Freeze

The final freeze for this phase of ENCODE will be July 2012. The pipeline will close at the end of July, and the DCC will be focusing on data review and release through the month of August. Procedures for data submission after August 1 will be developed by the new DCC, and will be communicated to the labs when they are available. Please try to submit data for this freeze as soon as possible.

Data Submission and Track Status

The most recent spreadsheet of hg19 submissions as reported by the pipeline automation is: Media:EncodeExperiments.2012-05-15.xlsx

Reports from the DCC wranglers regarding hg19 track status are here: HG19 Track Status

Tracks released this month on the UCSC public site

  • Caltech RNA-Seq (release 3) Fix release
  • FSU Replication Timing
  • RIKEN CAGE Loc (Release 3)
  • SYDH TFBS (Release 2)

Tracks currently under review by the DCC quality group

  • GIS ChIA-PET FINAL
  • Txn Factor ChIP (Release 2)

The complete list of released ENCODE tracks

Mouse ENCODE

Data Submissions and Track Status

The latest spreadsheet of Mouse ENCODE experiments submitted to the DCC is: Media:MouseExperiments.2012-05-15.xlsx

Mouse track status from wranglers is here: MM9 Track Status

Tracks released this month on the UCSC public site

  • Caltech RNA-Seq (release 1, final)
  • LICR RNA-Seq (Release 2)
  • PSU Histone


The complete list of ENCODE data at GEO

Outreach

UCSC, Ensembl and GENCODE presenters jointly presented a day-long workshop on 'Working with ENCODE Data' to 30 participants at Cold Spring Harbor lab, immediately preceding the Biology of Genomes meeting at Cold Spring Harbor Laboratory.

Other

  • The new Experiment Matrix application was released this month. A version for Mouse ENCODE will be available soon ( beta version will be available on preview browser on Monday):
 http://genome-preview.ucsc.edu/ENCODE/dataMatrix/encodeDataMatrixMouse.html
  • The new Software Tools portal page with content from Mike Pazin has been released. The Quality Metrics page is in preparation.