I have two replicates of RNAseq data for four different condition (one unstimulated and three different stimulation) with and without a transcription factor(TF) Knock down and ChIPseq data of this factor in all these four condition. I would like to study the effect of stimulation, knock-down and TF binding. what approach/analysis i should take to address my question. I know this is very broad question, any suggestion/guidance will be appreciated.
Note: I have already analyzed RNASeq data and ChIPseq data and have expression and binding information with me.