I've a question about ChIP-seq and how to use the controls.
I've already done the ChIP and it's been sequenced, so far so good.
Now, one way or another the IGG controls are not available. What we are left with are the two antibodies of interest, a histone modification (closed chromatin) antibody, and no-antibody (input undergone the ChIP experiment - apart for the antibody part).
-All of the above in duplicates - also, the chip was done with a magnetic beads-kit.
The big question is, do we use the no-antibody for noise removal ? Or do we use the closed chromatin, knowing that by removing all the peaks coming from it we remove both the noise and possible coinciding peaks?
This is a much debated issue in my lab at the moment, so any help/suggestion/reference to a paper would be extremely appreciated!
Thanks a lot in advance