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2012-03-16 DCC Progress

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Data Submission and Track Status

The current data freeze for ENCODE ends at midnight PST on Friday March 30. This is a hard freeze. At that time the pipeline will be closed for post-freeze processing and pipeline maintenance. We estimate 2 weeks down-time.

The pipeline reporting currently shows 2585 experiments on hg19/GRCh37, an increase of 258 over last month. The most recent spreadsheet of hg19 submissions as reported by the pipeline automation is: Media:EncodeExperimentsHg19.2012-03-15.xlsx

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

  • Broad Histone (Release 2)
  • CSHL Sm RNA-seq (Release 2)
  • GENCODE V10
  • GENCODE V11
  • HAIB RNA-seq
  • HAIB TFBS (Release 2)
  • UW CTCF Binding (Release 3)
  • UW DNase I HS (Release 4)
  • UW Histone (Release 3)

Tracks currently under review by the DCC quality group

  • UMass 5C Interactions hg19

Next tracks for review

  • LICR RNA-Seq (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.2012-03-15.xlsx

Mouse track status from wranglers is here: MM9 Track Status

Tracks released this month on the UCSC public site

  • CSHL Long RNA-Seq

ENCODE data accessioned at GEO this month

CshlShortRnaSeq - additional data added GSE24565

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.