Cut&Run: E-coli spike-in
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 !
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