ChIP-seq data for H3K9me3 in TIG3 cells without HU treatment
Raw reads were aligned to the human genome (hg19 assembly excluding non-canonical chromomes i.e. random, unknown and haplotype variant chromosomes) using Bowtie version 0.12.7 with default parameters except '-S -m 1', which excludes reads mapping to multiple chromosomal positions. Peak detection was performed with MACS2 version 2.0.9 (20111102) using default settings except for parameters '--broad --nomodel --shiftsize=110'. The shift size of 110 bp was calculated as the median over all Phantom Peak (Kharchenko et al. 2008)shift estimates for our H3K9me3 samples. When running differential peak detection between two H3K9me3 samples in MACS2 the additional parameter '--shift-control' was specified. Bigwig files were generated using the UCSC Kent utilities(Kent et al. 2010). We allowed only one read per chromosomal position thus eliminating potential spurious spikes, and each remaining read was extended from its 5-end to a total length of 250 bases, before converting to bedGraph format, scaling to mapped reads per million and final convertion to bigwig format.