Question: Setting up analysis for RIPSeeker correctly
0
gravatar for snamjoshi87
3.1 years ago by
snamjoshi8730
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
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 16.09
Traffic: 129 users visited in the last hour