Question: Documentation for HotSpot Peak Caller
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gravatar for taraeicher
12 days ago by
taraeicher10
taraeicher10 wrote:

This will probably seem like a silly question, but I would like to know if anyone has access to a current version of the HotSpot documentation. I am trying to run SPOT on a BAM file. I have checked the README from the HotSpot GitHub repo ( https://github.com/rthurman/hotspot/tree/master/hotspot-distr ), but it does not give much detail and references a broken link as the full documentation. Furthermore, cloning the repo and running the SPOT script without parameters or with --help does not give any useful information on how to run the program.

ADD COMMENTlink modified 12 days ago by ATpoint23k • written 12 days ago by taraeicher10

Can confirm the link is broken. I strongly suggest to avoid software that is poorly documented (and probably not maintained anymore, the last Git commit is > 6 years old). For which application do you need the tool, there are for sure good alternatives?

ADD REPLYlink written 12 days ago by ATpoint23k

I want to verify that my DNase-seq assays meet ENCODE standards using the SPOT score: https://www.encodeproject.org/data-standards/dnase-seq/. To my knowledge, only HotSpot reports SPOT scores, but if anyone knows of another type of software for this purpose, that would be great.

ADD REPLYlink written 12 days ago by taraeicher10
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