Tutorial

In this tutorial, we are going to show how to use HINT for identification of footprints using open chromatin assay and differential footprint analysis.

Footprints calling

In order to perform footprints identification using ATAC-seq

Download here. Execute the following commands in order to perform footprints identification from ATACseq data:

cd HINT_ATACTest
rgt-hint --atac-footprints --output-location=./ --output-prefix=test ATAC.bam ATACPeaks.bed

Histone footprinting Test

Download here. Execute the following commands in order to perform footprints identification from histone modification data:

cd HINT_HistoneTest
rgt-hint --histone-footprints --output-location=./ --output-prefix=test histone.bam histonePeaks.bed

DNase+Histone footprinting Test

Download here. Execute the following commands in order to perform footprints identification from DNase-seq combining with histone modification data:

cd HINT_DNaseHistoneTest
rgt-hint --dnase-histone-footprints --output-location=./ --output-prefix=test DNase.bam H3K4me1.bam H3K4me3.bam regions.bed