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Altius / hotspot2

Implementation of hotspot2 by Eric Rynes
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no peaks #1

Closed sjneph closed 8 years ago

sjneph commented 8 years ago

There aren't peak calls in the pipeline. These require densities, and have a dependence upon modwt (possibly others). Peaks-per-hotspot is a necessary add-on.

Are we doing the badspot heuristics to filter out microrna effects?

fwip commented 8 years ago

AFAIK, we're not using any badspot heuristics.

We do ask the user for sites to exclude, so as a workaround for now, a user could run the badspot finder and merge it with their exclude regions file before providing it to hotspot2.sh.

sjneph commented 8 years ago

added the peak caller and peaks-per-hotspot. There is still some work somewhere probably, but it's in pretty good shape. Closing this issue.