Cut&Run: E-coli spike-in

Question

[kim]

Hello everyone!

I've run the nf-core Cut&Run pipeline on five samples, each with three replicates, using IgG as a control and an E. coli spike-in for normalization. The pipeline normalization was set to spike-in.

I'm now planning to conduct differential analysis with DiffBind and have included the spike-in BAM files in my sample sheet.

Could someone please advise on the appropriate parameters for dba.normalize, or should I skip this step since spike-in normalization was already applied in nf-core Cut&Run?

Thank you so much !

[Ram]

Please don't use ALL CAPS - it's the online equivalent of yelling. I've fixed it for you this time/