Chunk #58 — Online Methods — 1. Data matrix, primary analysis and processing, quality control — 1.2 ChIP-seq and DNase-seq uniform reprocessing for consolidated epigenomes — e. Quality Control
For the primary Release 9 datasets, data quality enrichment scores were computed as the fraction of the uniquely mapped reads overlapping with areas of enrichment. Several methods were employed to select signal enrichment regions. The SPOT quality score was computed based on regions identified with the HotSpot peak caller103; the FindPeaks quality score was inferred based on peak calls made using the FindPeaks36 software; finally, a Poisson metric was derived by modeling the read distribution in genome-tiling 1000 basepair windows with a Poisson process and selecting as enriched regions windows with p < 0.05. All the quality scores in Release 9 are in agreement, with strong pairwise correlation (Pearson correlation > 0.9). Concordance between centers was confirmed and data analysis pipeline was validated at the outset of the project using datasets for the H1 cell line. The same pipeline was subsequently used to produce Release 9 data. ChIP-seq data for 6 histone modifications (H3K4me3, H3K27me3, H3K9ac, H3K9me3, H3K36me3, and H3K4me1) were independently generated for the H1 cell line by three REMCs (Broad, UCSD, UCSF-UBC). To quantify concordance, the reads from
