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ENCODE DNase-seq Peaks and Signal of Open Chromatin based on Uniform processing pipeline

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 Configure 		 Peaks  1  GM12878  UW-Duke  GM12878 DNaseI FDR 1% Uniform Peak Calls from UW-Duke    Data format 
 
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Assembly: Human Feb. 2009 (GRCh37/hg19)

Note: ENCODE Project

Description

This set of data tracks represents the set of Open chromatin elements and signals based on DNase-seq data from the Duke University and University of Washington (UW) production groups. The data tracks were generated by the ENCODE Analysis Working Group (AWG) based on a uniform processing pipeline. The datasets are based on the January 2011 internal data freeze. These datasets were used in all downstream analysis pipelines by members of the ENCODE Consortium and are one of the primary sources of data referenced in the ENCODE Integrative analyis paper (ENCODE Project Consortium, 2012).

Methods

To reduce a source of variability between UW and Duke DNaseI processed datasets, the Stam Lab (UW) did the following with the Duke DNase-seq aligned reads, to more closely match UW processing:

  • Combined all replicates for a given cell type
  • Subsampled the result at a level of 30 million tags
  • Ran results through the Stam Lab hotspot pipeline

First, hotspots (i.e. broad, variable-sized regions of generalized chromatin accessibility) were identified using a relaxed threshold. FDR 1% peaks (narrowPeaks) were generated by first thresholding hotspots (using random simulation) at FDR 1%, and then locating local maxima of the tag density (150 bp window, sliding every 20 bp) within the hotspots. FDR 1% peaks were set to a fixed width of 150 bp.

The combined calls are just a union of the calls for both groups, except for those 14 cell types where both groups have data. In the latter case, a collapsed set of FDR 1% peaks were generated by taking a non-overlapping selection of the calls from both centers and giving preference to the peak with the higher z-score when calls overlapped. A collapsed set of hotspots on these cell types was generated by simply merging the calls from both centers (taking the union interval of overlapping intervals).

Uniform signal was generated by processing the aligned reads using the align2rawsignal "Wiggler" software (see http://code.google.com/p/align2rawsignal for details and settings). The method accounts for the depth of sequencing, the mappability of the genome (based on read length and ambiguous bases) and different fragment length shifts for the different datasets being combined. It also differentiates between positions that showed zero signal simply because they are unmappable and positions that are mappable but have no reads.

Data Release Policy

Data users may freely use ENCODE data, but may not, without prior consent, submit publications that use an unpublished ENCODE dataset until nine months following the release of the dataset. This date is listed in the Restricted Until column on the track configuration page and the download page. The full data release policy for ENCODE is available here.

There is no restriction on the use of these specific tracks.

References

ENCODE Project Consortium. An integrated encyclopedia of DNA elements in the human genome. Nature 2012 Sep 6;489(7414):57-74.

Contact

Bob Thurman