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Incorporate spike-in normalisation for macs2 peakcalling #200

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ClaireXinSun opened this issue Jun 2, 2023 · 2 comments
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Incorporate spike-in normalisation for macs2 peakcalling #200

ClaireXinSun opened this issue Jun 2, 2023 · 2 comments
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enhancement Improvement for existing functionality

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@ClaireXinSun
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Description of feature

Hi all, I am wondering what is the input for macs2 in the pipeline. From what I can see, if I choose macs2 as peakcaller, it uses the bam files, which is not normalsied by spike-in. SEACR used the bed files output from bamcoverage, which have been normalised to spike-in. Does it mean the output from MACS2 are actually skipped spike-in normalisation? Thanks.

A previous issue in MACS github give some ideas using 'bdgopt' subcommand
macs3-project/MACS#356
@ClaireXinSun ClaireXinSun added the enhancement Improvement for existing functionality label Jun 2, 2023
@svbekaer
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Hi Claire,
Did you get any answers on this one?
Thanks!
Sarah-Lee

@chris-cheshire
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chris-cheshire commented Nov 24, 2023 •
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I missed this somehow sorry, we spike-in normalise for both peak callers if that feature is active. The normalisation happens at the conversion from bam to bedgraph.

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@chris-cheshire @ClaireXinSun @svbekaer