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Question: Metrics for exploring the parameter space of broad domain chip-seq finders?
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Let us say I have want to use SICER or MACS2 for finding broad domains in ChIP-seq data. These contain plenty of parameters I can tune to change the domains found.

Are there any metrics I can use to see if some parameters perform better than others? Any idea, no matter how seemingly stupid, would be appreciated. If these metrics can be machine inspected so that I can automatically choose parameters that would be preferable, but any suggestions welcome.

ADD COMMENTlink 4.0 years ago Endre Bakken Stovner • 880 • updated 4.0 years ago dariober 10k
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This is my answer also to your previous question https://www.biostars.org/p/176736/.

At the end of the day, my way of assessing the quality of the ChIP and peak calling is to open ChIP and inputs in IGV and look at a few peaks taken from the high confidence to the lower confidence spectrum. Then check if they "look right". I know, it's subjective, it's not scalable. It sucks.

I was kind of writing a program (https://github.com/dariober/genomeGraphs) to at least simplify the scanning of peaks since scrolling through IGV can be painfully slow.

ADD COMMENTlink 4.0 years ago dariober 10k
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I already starred your repo. Since I use Python, I might go with meta-seq, but great job all the same!

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Endre Bakken Stovner
• 880

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