Q: Filtering blacklisted regions when using macs3 hmmeratac

[eggrandio]

Hello,

I do not see an option to filter out blacklisted regions when using hmmeratac. In the original hmmratac paper they state that this is a crucial step.

Should I remove the reads mapping to these regions beforehand ?

[taoliu]

Hi @eggrandio Thanks for asking! Please use -e or --blacklist option to filter out blacklisted regions. Forgot to add this option to the Essential options section of the online document. But you can still see the option in command line by typing macs3 hmmratac -h. We will add it in the next update of the documents.