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Application of LOCKs updated framework to define COREs #10

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reskejak opened this issue Feb 9, 2021 · 1 comment
Open

Application of LOCKs updated framework to define COREs #10

reskejak opened this issue Feb 9, 2021 · 1 comment

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@reskejak
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reskejak commented Feb 9, 2021

A general theory question: can/should the updated CREAM framework (used to define LOCKs) also be used to define COREs on accessibility data?

From my understanding, the CREAM_Cutoff iterations just identify an optimal WScutoff threshold, i.e. the optimal window size within the empirical distribution. This suggests to me that this optimization would also improve detecting canonical COREs as well. Further this framework could be practically applied to cluster peaks from almost any chromatin feature (not just modified lysine residues), I would guess.
@alimadani
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Great question! The optimization is useful for ChIP-seq data and when different profiles (different histone profiles) need to be compared. But I suggest you continue using it without optimization for CORE identification.

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@alimadani @reskejak