Hi all,
I am new to analysis of Chip-seq datasets, so I want to ask you a very naive question. I have 5 Chip-seq datasets for a transcription factor (A) but they are from different cell lines like LCL, BCBL. I want to know the genes/pathways targeted by this TF and also the DNA motif to which this TF may bind. I want to ask you that after peak calling will it be feasible to merge the peaks from these 5 datasets to get the consensus peaks (occurring > 3 datasets) and then doing the downstream analysis on the consensus peaks? Or I need to do some kind of normalization/correlation analysis before merging these?
In another case, I have datasets from different tissues and I want to do the same kind of analysis for this TF as well.
Thanks in Advance
