Cut&Run replicates handling

Question

[g.anande]

Is there a CUT&RUN peakcaller that supports replicates? If not, what is your recommended approach for handling replicates?

It appears that all available peak callers, such as SEACR, are designed to call peaks from single pull-down experiments.

Our Experiment: We have two conditions, Untreated (UTR) and Treatment (TREAT), each with two biological replicates. Each condition also has respective INPUT data for normalization.

We have completed:

• Quality Control (QC)
• Alignment
• Duplicate marking/removal
• Spike-in Calibration

Next, we would like to proceed to peak calling and differential analysis. We would appreciate your recommendations on suitable peak callers and the best practices for handling replicates.

Answer 1

[Asaf]

You can use nf-core cutandrun pipeline, it supports replicates in the step of consensus peaks calculations.

[ATpoint]

It's just an awk merge thing they do, not any replicate-aware calling, no?

[Asaf]

It's essentially bedtools merge of all the replicates. Definitely not replicate aware calling. I'm not sure it's necessary but I don't have a good enough understanding of the experimental setting and how different the replicates are.