For ChIP-seq analyis, Is it okay to use spike in normalization (Rx) and RPGC normalization together in the analysis pipeline?
If we use only Rx normalization alone, we get huge variation in the metagene plot between two biological replicates. Therefore, it is trickier to disect if it is due to biological variation or technical issue.But, if we try both Rx+RPGC normalization together, the variation is smaller, as it is what we expect. I was wondering if we can do two normalization together. I also need to mention that we see differences in the sequencing read depth between biological replicates.
Looking forward to your suggestions.