Question: Documentation for HotSpot Peak Caller
gravatar for taraeicher
12 days ago by
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 ( ), 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: 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
Please log in to add an answer.


Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1918 users visited in the last hour