There seems to be a disconnect between what I think should be required to publish ChIP-seq data and what I see published in a lot of papers. When I am reviewing papers I get that feeling that I am that jerk reviewer who's request go beyond what is reasonable, so I usually tone my comments down to closer to what I see published.
As with most stuff the bar will be raised as broader scientific community gains a better understanding of the pitfalls of the assay. Just like the first ChIP-seq papers seem completely inadequate today.
Here are some issues I think are worth discussing:
1) What is enough depth and how is it determined?
2) What are the mandatory controls. Input (my preference) but others use IgG.
3) Is one antibody enough? I don't think so because it doesn't control for antibody cross-reactivity.
4) Validation of data. Most people seem to pick their top peaks and check by qPCR, is that okay?
5) Number of replicates. They should be biological replicates in my opinion.
In order to avoid being that unreasonable 'third reviewer' and also to make sure the stuff being published is true, I'd like to hear people's opinions.
As with most stuff the bar will be raised as broader scientific community gains a better understanding of the pitfalls of the assay. Just like the first ChIP-seq papers seem completely inadequate today.
Here are some issues I think are worth discussing:
1) What is enough depth and how is it determined?
2) What are the mandatory controls. Input (my preference) but others use IgG.
3) Is one antibody enough? I don't think so because it doesn't control for antibody cross-reactivity.
4) Validation of data. Most people seem to pick their top peaks and check by qPCR, is that okay?
5) Number of replicates. They should be biological replicates in my opinion.
In order to avoid being that unreasonable 'third reviewer' and also to make sure the stuff being published is true, I'd like to hear people's opinions.
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