Question: Setting up analysis for RIPSeeker correctly
gravatar for snamjoshi87
3.1 years ago by
snamjoshi8730 wrote:

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:

Condition WT KO
Drug 1 3 1
Drug 1+2 3 3
Control 1 3 3
Control 2 2 0
Input 3 0

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.


ripseeker • 405 views
ADD COMMENTlink written 3.1 years ago by snamjoshi8730
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