Okay this is an open question for getting some ideas.
Imagine if you have a ChIP sequencing data on some disease say Type 2 diabetes (strictly for the sake of example) and you have this data from 3 different labs, which means three different sets of data on 3 different cell types.
(This ChIP sequencing data is on binding of a transcription factor X in a diseased state).
As an bioinformatician what you will first aim to get out of this data, I mean in terms of your goal(s).
Offcourse you will look for the regions which are conserved across the cell lines and the regions which are not unique.
But what will be your generic plan to get the most out from a dataset like this.
All suggestions are welcome.