I have four samples.
1) A standard ChIP for a transcription factor (TF) of interest.
2) A standard Input DNA control (i.e. sheared, but no IP).
3,4) Same as 1&2 but from Knockout cells completely lacking the TF.
What's the best way to utilize these controls?
I have been running peak callers using the Input DNA as control (i.e. 1 vs 2, and 3 vs 4). Then I subtract the overlapping peaks found in the knockout peak calling data from those in the wild-type.
Would it be better to run the peak analysis using just 1 vs 3 (i.e. wild-type ChIP vs knockout ChIP)? What's the ideal way to do this?
Thanks for any ideas
1) A standard ChIP for a transcription factor (TF) of interest.
2) A standard Input DNA control (i.e. sheared, but no IP).
3,4) Same as 1&2 but from Knockout cells completely lacking the TF.
What's the best way to utilize these controls?
I have been running peak callers using the Input DNA as control (i.e. 1 vs 2, and 3 vs 4). Then I subtract the overlapping peaks found in the knockout peak calling data from those in the wild-type.
Would it be better to run the peak analysis using just 1 vs 3 (i.e. wild-type ChIP vs knockout ChIP)? What's the ideal way to do this?
Thanks for any ideas
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