Sorry if this is a stupid question but I've been looking through the documentation and the manual and I'm not sure if I'm doing this correctly.
From what I can tell, RIPSeeker allows you to compare BAM files for an experimental condition against a control condition. Generally, this control condition would be background binding. But what if I want to compare to other conditions AFTER taking into account background binding? Here is my experiment setup with the numbers indicating replicates:
So my first question is: Should I be comparing my samples to the input or to the knockout?
Second, how can I set up RIPSeeker to make the following comparisons:
- Drug 1 v. Control 1 (after taking into account KO background for each)
- Drug 1+2 v. Control 1 (after taking into account KO background for each)
- Drug 1 v. Drug 1+2 (after taking into account KO background for each)
- Control 1 v. Control 2
The reason I am confused is that appears that RIPSeeker only takes two inputs: The BAM files for the experimental condition and the BAM files for the KO/background as specified by the "cNAME" argument. How, then, could I compare Drug 1 v. Control 1 for example after taking into account the KO background?
I hope this makes sense. I'm new to this kind of analysis so I may just be asking the wrong questions entirely.