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vierstralab / footprint-tools

A toolset to analyze genomic footprinting data
GNU General Public License v3.0
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what should I use for interval.bed file? #23

Closed shintarok111 closed 5 months ago

shintarok111 commented 5 months ago

I am trying to create a dispersion model with my data. I've read the documentation but couldn't find specific information about the interval.bed file. Does this file represent the BED file containing the lengths of each chromosome, or does it refer to a hotspot or peak.bed file that is generated by hotspot2?

Thank you for your kind assistance.

jvierstra commented 5 months ago

The interval file is a file of the genome regions that defines where you would like to identify footprints. Typically we use the peaks from a peak caller (hotspot2; https://github.com/Altius/hotspot2, or other).

shintarok111 commented 5 months ago

Thank you for your reply!