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Old 04-04-2013, 01:24 AM   #1
Tobikenobi
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Location: Japan

Join Date: Mar 2013
Posts: 17
Default When to integrate the negative control?

Dear all,

I am working on a transcription factor Chip-Seq analysis that includes the following samples:
1. IP replicate 1
2. IP replicate 2
3. IgG negative control
4. Input

When is it suitable to include the IgG in the analysis process?
By that I mean, once I have called peaks of my replicates vs the Input, should I call peaks in IgG vs Input, or/and does it make sense to call peaks in the replicates vs IgG?
My first guess would be to call peaks all samples vs the Input and then substract the peaks found in IgG, but any comment is much appreciated!
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