Calculating necessary coverage for ChIP-seq

OK, so you have a genome — let’s say it’s about 1gb in size — andyou want to do ChIP-seq on a transcription factor that you thinkbinds ~1000 places in the genome. You’ve measured the specificityof the transcription factor and it seems to enrich about 10-foldover background (an OK but not fantastic number). How much sequencingdo you need to do to see a statistically significant signal?

We need two other numbers. First, what fragment size are you going touse? And second, what level of signal over background do you want tosee?

Back of the envelope calculations from Titus on how much short read sequencing to do for a ChIP-seq experiment. These types of calculations are extremely useful since they force you to lay out your assumptions before starting the experiment. When your results differ from the calculations, cycling back to understand the results is much quicker since you’ve already thought through the problem.


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