>I promised a quick discussion on ChIP-Seq and controls, as well as a comparison of FindPeaks with USeq, though I may have to defer on the second topic. I haven’t played much with USeq, though I did look through it’s code several months ago. I think I’d best keep my comments to a minium and say only that ChIP-Seq software evolves quickly, and that it’s a moving target. Comparing FP 126.96.36.199 would be doing a disservice to my code, which was tagged several months back, while USeq is being developed out in the open, and you can get a copy of what the developer was working on last night. Truly an unfair comparison. I think I’ll revisit this topic when I release FP 4.0.
The other topic is the use of controls. It’s an area that everyone at GSC acknowledges we could do better in. It’s just common sense that you’d want controls – this is science, after all.
However, there are different types of controls. Do you want a control that simulates a null-antibody? Do you want a genomic control that leaves out the ChIP entirely? Possibly there are other kinds I haven’t even though about, and they are all “valid” controls for different things in a ChIP-Seq experiment.
Which brings up the really key point: there are more things going on in ChIP-Seq than just peaks, and you can’t completely ignore all of them, just to filter out peaks that are found in your control. That’s a relatively naive method that other groups used several months ago. (I don’t know if they’re still using them.) I believe “Singapore” was using controls simply by checking if each peak’s maximum had a greater than 4:1 ratio over the same base location in their control and throwing away anything that didn’t pass that criteria. I believe other labs are doing similar things.
Anyhow, I think it’s safe to say that such a simple method is a great first pass (and yes, ALL of us are on our first pass, at the moment, so it’s definitely not an insult), but I don’t think this will stand the test of time.
For now, when I get a few minutes, I’m going to start working on integrating controls into FindPeaks 4.0. As of this morning, I ran the first few successful PET runs with the software, so work on controls won’t be that far off.