Scaling normalisation for ChIP-seq with exogenous chromatin Workshop - PowerPoint PPT Presentation

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Scaling normalisation for ChIP-seq with exogenous chromatin Workshop on ChIP-seq data analysis Stockholm, 9 November 2018 Agata Smialowska NBIS, SciLifeLab, Stockholm University Local vs. global change in abundance Global difference due to *

Scaling normalisation for ChIP-seq with exogenous chromatin Workshop on ChIP-seq data analysis Stockholm, 9 November 2018 Agata Smialowska NBIS, SciLifeLab, Stockholm University
Local vs. global change in abundance Global difference due to * global change in signal * technical issue B: scaling to library size C: B & quantile normalisation D vs. E: D: technical issue E: genuine difference Bonhoure et al , 2014
Global change in abundance Orlando et al , 2014
Global change in abundance
The principle of scaling normalisation • Scaling to number of mapped reads in exo chromatin • Scaling to average background in exo chromatin
Things to be aware of … • Chromatin quantification • Different IP efficiency for exo- and endo- chromatin dm6 hg38 H3K79me2 content: ChIP: 57 > 59 > 61 ; Input: 89 > 91 > 93

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