Hi all,
I am a beginner working on CUT&RUN data analysis and following the tutorial (Hands-on: CUT&RUN data analysis / CUT&RUN data analysis / Epigenetics). I’d like to perform spike-in normalization as part of the workflow. I’ve already mapped reads to spike-in genome(S. cerevisiae) and calculated scaling factor by dividing the number of reads aligned concordantly exactly once by the total number of reads.
Now, I am trying to figure out how to apply this scaling factor to normalize BAM files within galaxy, before proceeding to peak calling.
Any help would be greatly appreciated!