Hi,

We have performed a ChIP-seq experiment in S. cerevisiae with two conditions (control and mutant) using S.pombe as a spike-in (because the antibody works in both organisms). The reason because we add spike-in is that the antibody is not very efficient so we wanted to normalise the immunoprecipitation efficiency between samples in some way. But we would like to add another normalization step as TMM because the library size is very different between conditions (mutant condition accumulate most of the reads in repetitive regions that we are no able to map) and we expect a small portion of regions to be differentially enriched.

Does anyone knows how should we proceed?

Thanks in advance

It is impossible to use both spike-in or TMM normalization. You must do one or the other. They replace each other, they cannot be combined.

TMM normalization is independent of whether the library sizes are different or not. edgeR always normalizes for library size and that is separate from TMM normalization.

I would recommend spike-in normalization only when there are likely to be massive global changes in binding, i.e., when more than half of regions are differential in the same direction. If you expect only a small portion of regions to be differentially enriched, then spike-in normalization is unnecessary and highly counter-productive and will simply add noise to your experiment.

I don't follow the background you give. You say that there is massive change of where the reads are mapped between mutant and control but you also say that only a small portion of regions to be differentially enriched. How can that be true? If it was true, then why would you not simply use TMM, which is designed for exactly that scenario?