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kundajelab / basepairmodels

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Is BPNet appropriate for modeling histone modification ChIP-seq data? #37

Closed stephenrong closed 4 months ago

stephenrong commented 4 months ago

Such as H3K27ac, H3K4me3, and H3K4me1 data. Or would be it inappropriate to use for some reason, such as a larger average peak size, some technical bias I might not be aware of, or non-discoverability of the underlying regulatory grammar, compared to TF ChIP-seq?

akundaje commented 4 months ago

No it will not work well as is on histone marks. We'll have a powerful histone mark model out in a few months.

On Fri, Jun 7, 2024, 7:18 AM Stephen Rong @.***> wrote:

Such as H3K27ac, H3K4me3, and H3K4me1 data. Or would be it inappropriate to use for some reason, such as a larger average peak size, some technical bias I might not be aware of, or non-discoverability of the underlying regulatory grammar, compared to TF ChIP-seq?

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stephenrong commented 4 months ago

Thanks, looking forward to it!