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2012-06-15 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.2012-06-14.xlsx. Pipeline reporting shows a total of 2745 experiments submitted on the hg19 genome assembly.

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

Tracks released this month on the UCSC public site

  • GIS ChIA-PET
  • UW DNase I HS (Release 5)

Tracks currently under review by the DCC quality group

  • CSHL Long RNA-seq (Release 2)
  • SYDH Histone (Release 3) FINAL
  • UCSC Regulation Transcription Track (release 2)

Next tracks for review

  • CSHL Sm RNA-seq (Release 3)

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.2012-06-14.xlsx. Pipeline reporting shows a total of 507 experiments submitted on the mm9 genome assembly.

Mouse track status from wranglers is here: MM9 Track Status

Tracks currently under review by the DCC quality group

  • Stan/Yale TFBS (Release 3)

ENCODE data accessioned at GEO this month


The complete list of ENCODE data at GEO

ENCODE and modENCODE Data Listings

  • Human Production ENCODE PID: 63441
  • Mouse ENCODE PID: 50617


Other

  • The Experiment Matrix application for Mouse ENCODE data was released this month:
 http://genome-preview.ucsc.edu/ENCODE/dataMatrix/encodeDataMatrixMouse.html
  • The Quality Metrics page for Human ENCODE data is under review and will be on the preview browser at week's end. It is accessed from the Data Standards page.