Chunk #50 — Online Methods — 1. Data matrix, primary analysis and processing, quality control — 1.2 ChIP-seq and DNase-seq uniform reprocessing for consolidated epigenomes — b. Mappability filtering, pooling and subsampling
The raw Release 9 read alignment files contain reads that are pre-extended to 200 bp. However, there were significant differences in the original read lengths across the Release 9 raw datasets reflecting differences between centers and changes of sequencing technology during the course of the project (36 bp, 50 bp, 76 bp and 100 bp). To avoid artificial differences due to mappability, for each consolidated dataset, the raw mapped reads were uniformly truncated to 36 bp and then refiltered using a 36 bp custom mappability track to only retain reads that map to positions (taking strand into account) at which the corresponding 36-mers starting at those positions are unique in the genome. Filtered datasets were then merged across technical/biological replicates, and where necessary to obtain a single consolidated sample for every histone mark or DNase-seq in each standardized epigenome. Table S1. summarizes the mapping of the individual Release 9 primary data sample files to the consolidated data files corresponding to the 127 consolidated reference epigenomes.
