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Please go to the ENCODE3 wiki for current information.

2012-04-20 DCC Progress

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Data Submission and Track Status

The March 2012 data freeze for ENCODE ended at midnight PST on Friday March 30. The pipeline reopened at 9am PST on Monday April 16. All data from the freeze has been processed and the DCC team was able to make significant progress improving validation software in the pipeline. Thanks to all for a successful freeze. Production groups please thanks your wranglers.

The pipeline reporting currently shows 2743 experiments on hg19/GRCh37, an increase of 158 over last month. The most recent spreadsheet of hg19 submissions as reported by the pipeline automation is: Media:EncodeExperimentsHg19.2012-04-18.xlsx (Note: this version has Mar2012 freeze reported for all datasets after previous freeze -- this will be corrected).

The real-time reporting is now linked on to the left menu bar for easy access.

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

Tracks released this month on the UCSC public site

  • Duke Affy Exon (Release 3)
  • Duke DNaseI HS (Release 2)
  • ENCODE Pilot (pilot regions mapped to hg19)
  • UMass 5C
  • UW Histone (Release 4)

Tracks currently under review by the DCC quality group

  • Caltech RNA-Seq (Release 3)
  • GIS ChIA-PET
  • Txn Factor ChIP (Release 2)

The complete list of released ENCODE tracks

Mouse ENCODE

Data Submissions and Track Status

The automated reporting currently shows 481 experiments, an increase of 56 over last month.

The latest spreadsheet of Mouse ENCODE experiments submitted to the DCC is: Media:MouseExperiments.2012-04-18.xlsx

Mouse track status from wranglers is here: MM9 Track Status

Tracks released this month on the UCSC public site

  • LICR Histone (Release 2)
  • LICR TFBS (Release 2)

Next tracks for review

  • LICR RNA-Seq (Release 2)
  • PSU Histone

ENCODE data accessioned at GEO this month

The complete list of ENCODE data at GEO

Outreach

UCSC, Ensembl and GENCODE presenters will be jointly teaching a day-long workshop on 'Working with ENCODE Data' on May 8, preceding the Biology of Genomes meeting at Cold Spring Harbor Laboratory. Many thanks to Jen Harrow at the Sanger for initiating and organizing this workshop.

Other

The DCC has some major improvements to the portal scheduled for this month:

  • new pages for Software Tools and Quality Metrics are in preparation. Thanks in advance to Mike Pazin for this valuable content.