Hi all, I'm currently trying to work off part of a paper (found here) involving processing some ChIP-seq data for histone modifications (ie H3K4me1). At one point (under "Histone Modication Inputs, Normalization, Preprocessing") the authors say:
The ChIP-seq reads of these histone modifications were binned into 100bp intervals and normalized against its corresponding inputs by using an RPKM (reads per kilobase per million) measure.
I'm a bit confused as to how this could be replicated and what it means. My initial thought was to use a tool like deeptools bamCoverage to get a normalized (RPKM) value for 100bp bins. However, my understanding is that this is a normalization for sequencing depth - not a normalization against the ChIP-seq input. I thought I should then use bamCompare to compare the input vs targeted ChIP-seq, but it occurs to me that this will give me a ratio, not a RPKM value per bin. Could anyone explain what they mean by "normalized against it's corresponding inputs" in this case? Sorry if any of this is naive, I'm new to this and appreciate any help.