What Coverage Is Required For Chip-Seq Experiments?

Question

[Jeremy Leipzig]

How many short reads (<100bp) would you need for each sample to detect peaks for the average transcription factor in human? How many replicates?

"It depends" is not really an adequate answer unless you can provide a heuristic formula taking into account the dependencies. A rough estimate is fine.

I would also accept a literature review/meta-analysis.

[Jeremy Leipzig]

Looks like C. Titus Brown gave this a go.

Answer 1

[Sean Davis]

Unfortunately, it does depend. It depends at least on the enrichment of the antibody over background and on the binding pattern of the TF across the genome. Antibodies with lower (only a few fold) enrichment or TFs with a promiscuous binding pattern (bind all over the place) will require more reads. However, without any other information, a few million reads (a lane, for example) is a place to start. From there, you can do some virtual experiments to look at the added benefit of more reads by subsampling your data at various levels and observing the increase in numbers of sites picked up with increased coverage. If you see a plateau in the sites versus reads, then you are probably close to the number of reads that you need.

[Olbzn]

Check out Lefrancois, 2009 PMID:19159457 for a precise answer to your question (see table 5 especially)