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2012-02-17 DCC Progress

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Data Submission and Track Status

The next data freeze for ENCODE has been set for March 2012. Production groups are encouraged to submit data for this freeze by March 1, with a hard freeze at the month's end. As the last day of March falls on a Saturday, the DCC is setting the freeze cut-off for Friday night (March 30). The submission pipeline will close at midnight PST. The pipeline will close for 1 week for post-freeze processing. For pipeline maintenance purposes, the DCC would like to reserve an additional week of pipeline closure following the freeze (for a total of 2 weeks down-time). Production groups that find this problematic should contact us.

The pipeline reporting currently shows 2327 experiments on hg19/GRCh37, an increase of 28 over last month. The most recent spreadsheet of hg19 submissions as reported by the pipeline automation is: Media:EncodeExperimentsHg19.2012-02-15.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

  • HAIB Genotype (Release 2)
  • Open Chrom Synth (Release 2)
  • UW DNaseI DGF (Release 3)
  • UW Repli-seq

Tracks currently under review by the DCC quality group

  • HAIB TFBS (Release 2)
  • UW Histone (Release 3)
  • GENCODE V10

Next tracks for review

  • CSHL Sm RNA-seq

The complete list of released ENCODE tracks

Mouse ENCODE

Data Submissions and Track Status

The automated reporting currently shows 373 experiments, an increase of 24 over last month.

The latest spreadsheet of Mouse ENCODE experiments submitted to the DCC is: Media:MouseExperiments.2012-02-15.xlsx

Mouse track status from wranglers is here: MM9 Track Status

Tracks released this month on the UCSC public site

  • PSU TFBS

Information needed from Labs

Documentation is needed from these labs:

  • Stam: ChIP-Seq TFBS track

ENCODE data accessioned at GEO this month

New:

Note: Reserved GEO Numbers indicate that the DCC has made the initial steps to set the structure of ENCODE data in GEO and so that submission in the future can proceed smoothly

Reserved (hg19):

Submitted for reservation (mm9):

  • wgEncodeCaltechHist
  • wgEncodeCaltechTfbs
  • wgEncodeCshlLongRnaSeq
  • wgEncodeLicrRnaSeq
  • wgEncodeLicrTfbs
  • wgEncodePsuHistone
  • wgEncodePsuTfbs
  • wgEncodeSydhTfbs
  • wgEncodeUwDnase


The complete list of ENCODE data at GEO