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

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Sep 11, 2023 45 likes •109 views

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 *

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Scaling normalisation for ChIP-seq with exogenous chromatin

Stockholm, 9 November 2018 Agata Smialowska NBIS, SciLifeLab, Stockholm University

Workshop on ChIP-seq data analysis

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Local vs. global change in abundance

Bonhoure et al, 2014 B: scaling to library size C: B & quantile normalisation D vs. E: D: technical issue E: genuine difference Global difference due to * global change in signal * technical issue

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Global change in abundance

Orlando et al, 2014

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Global change in abundance

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The principle of scaling normalisation

Scaling to number of mapped reads in exo chromatin
Scaling to average background in exo chromatin

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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