Documentation for HotSpot Peak Caller

Question

[taraeicher]

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.

[ATpoint]

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?

[taraeicher]

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.

Answer 1

[taraeicher]

I never found the documentation, but I did find that many people use the broadpeak option in MACS2 to call hotspots. It is then possible to obtain the total coverage of hotspots using the output file. For anyone else following this post, I would recommend MACS2 as a better option than HotSpot, as it is still being actively maintained.