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ChIP-Seq heatmap generation

SB Sara Badodi
NP Nicola Pomella
XZ Xinyu Zhang
GR Gabriel Rosser
JW John Whittingham
MN Maria Victoria Niklison-Chirou
YL Yau Mun Lim
SB Sebastian Brandner
GM Gillian Morrison
SP Steven M. Pollard
CB Christopher D. Bennett
SC Steven C. Clifford
AP Andrew Peet
MB M. Albert Basson
SM Silvia Marino
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The deeptools algorithms bamCompare, bigWigCompare and plotHeatmap were used to produce relevant bigwig files and heatmaps, in order to assess region-wide and genome-wide coverage. Specifically, coverage tracks were first obtained by normalising each sample alignment file against the corresponding input (--operation log2ratio) and then pooled at both replicate and cell line levels (--operation mean), to obtain a representative sample for each antibody/condition. The regions chosen to be visualised in the heatmaps were those of consensus peaks (details in the figure legends), centred on their nearest TSS.

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