NOTE! This is a read-only copy of the ENCODE2 wiki.
Please go to the ENCODE3 wiki for current information.
2011-01-21 DCC Progress
January 2011 freeze
The January 11 data freeze ends TODAY, January 21, 2011. Important dates for this freeze are:
- January 21: Pipeline closure at Midnight PST, for 1 week intensive wrangler processing
- Feb 7-11: Data approval calls between production labs and DCC
Approval calls are scheduled here: January_2011_Data_Freeze#Data_Approval_Calls
The detailed freeze plan and expected submission spreadsheets are here: January_2011_Data_Freeze.
Data submission and track status
The pipeline reporting currently shows a total of 1354 (229 submitted this month) experiments validated on hg19. A spreadsheet of hg19 submissions as reported by the pipeline is: Media:EncodeExperimentsHg19.2010-01-20.xlsx
Some new datatype submissions that have been submitted for this freeze but are not yet sufficiently processed to appear in reporting are:
GIS ChiaPET (Ruan): 6 experiments: Pol2 in K562, Hela-S3, NB4, HCT-116 and MCF-7, and ER in MCF-7 UChicago TFBS (White): 7 experiments in K562: JunB, JunD, HDAC8, Fos, GATA2, NR4A1 and Control (tagged w/ eGFP) SYDH Nucleosome (Snyder): 1 experiment in K562
Reports from the DCC wranglers regarding hg19 track status are here:
The DCC quality group is currently reviewing the following hg19 and mm9 tracks for release to the public:
- Riken CAGE
- Caltech RNA-seq
- Stan/Yale TFBS (mm9)
- UW Histone
The next tracks for review will include:
- SUNY Tiling
- GIS RNA PET
- UW Affy Exon
Ready response by production groups to any issues arising during the Q/A process will help assure speedy release.
Recent data releases on hg19/GRCh37 from the UCSC Browser group are listed here:
- Early public access to ENCODE data: UCSC is completing deployment of a Preview Browser server (http://genome-preview.ucsc.edu). This server will be a mirror of genome-test, synchronized on a weekly basis.
- UCSC is updating the ENCODE portal to provide a more user-friendly interface, based on input from PI's and the ENCODE101 manuscript review. The current version (still under development) is viewable on genome-test.
- As of this reporting, a total of 87 experiments have been submitted and validated by the Mouse ENCODE groups. The latest spreadsheet of Mouse ENCODE experiments submitted to the DCC is: File:MouseExperiments.2011-01-20.xlsx
- For detailed status by track see: Mouse ENCODE track status Jan-20-2011
- The SYDH TFBS track (w/o CH12) is currently under review by Q/A group at the DCC, with release expected next week. This will be the first MOUSE ENCODE track to be released on the UCSC public site. The other Mouse ENCODE tracks on the test server will soon be publicly available on the UCSC Preview site (http://genome-preview.ucsc.edu), soon to be announced.
- As part of the ENCODE portal update in progress, a Mouse Data Summary page is under development. The initial version will host a snapshot of the submissions spreadsheet. We are planning to replace this with a more graphic matrix-oriented interface. The planning spreadsheet is also linked to this page.
- Work is in progress at the DCC to submit Mouse ENCODE data to GEO. GEO is setting up a Mouse ENCODE project to support this.
Information needed from Labs
- CH12 data is on hold until metadata is complete (DCC is advised regarding sex to register for the cell line).
- Documentation is needed from these labs:
Hardison: TFBS and Histone tracks Stam: DNase track Ren: TFBS and Histone tracks