CUT&RUN

[BADGERJL]

Hi team,

I am interested in how using deepTools for CUT&RUN compares with ChIP-seq data. I found tutorials on the ChIP-seq analysis using deepTools very helpful, particularly a YouTube video from your group discussing use for ChIP-seq. We are looking to compare CUT&RUN (specifically for H3K27ac) and I'm curious if I should be looking for generally the same metrics as ChIP-seq. For example, do the recommendations as far as interpretation of the plotFingerprint plots for coverage and target enrichment hold true for CUT&RUN (i.e. ideal having peak starting to rise around 0.1 to 0.2 to indicate good genome coverage?), or would the higher signal to noise ratio expected with CUT&RUN change the way we should interpret these graphs? Any other tips or resources for deepTools and CUT&RUN?

Because there is no Input equivalent, I'll be performing IgG control. I'm having trouble imagining if this would be expected to look more like an Input, but perhaps with lower coverage? Is plotFingerprint just not useful for CUT&RUN?

[Devon Ryan]

In general I would hope that cut and run would show much lower
background coverage than traditional ChIP-seq, so hopefully you won't
have any coverage of most of the genome. So yes, I think
plotFingerprint is still useful for this type of data, but I wouldn't
expect the same metrics (instead, I'd expect a higher X intercept and
elbow point). I'm curious to hear how your IgG data looks. My guess is
that you'll end up with little enough material that sequencing will be
difficult, similar to issues we usually have with IgG in traditional
ChIP-seq.

I think we'll be generating some cut and run data in 2020 as well, so
we'll have better recommendations at that point.

Devon
--
Devon Ryan, Ph.D.
Email: dpr...@dpryan.com
Data Manager/Bioinformatician
Max Planck Institute of Immunobiology and Epigenetics
Stübeweg 51
79108 Freiburg
Germany

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[BADGERJL]

Thanks for the expert input! I was thinking something similar, so glad to know I'm on the right track. Looking forward to comparing with any forthcoming CUT&RUN data using deepTools for QC!

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