#!/bin

#Find motifs using Homer
#Homer software: /projects/epigenomics3/epigenomics3_results/users/ajyzhu/Programs/Homer/bin/
# findMotifsGenome.pl <peak/BED file> <genome> <output directory> -size #


#CK
/projects/epigenomics3/epigenomics3_results/users/ajyzhu/Programs/Homer/bin/findMotifsGenome.pl /home/egibbard/epigenomics3/peak_called/blacklist_rm/50_percent_called_peak/CR_CK_CTCF.bl_rm_50.narrowPeak hg19 /home/egibbard/epigenomics3/peak_called/blacklist_rm/50_percent_called_peak/homer/CK_CTCF -size 200 #default

/projects/epigenomics/software/homer/bin/findMotifsGenome.pl /home/egibbard/epigenomics3/peak_called/blacklist_rm/50_percent_called_peak/CR_CK_CTCF.bl_rm_50.narrowPeak hg19 /home/egibbard/epigenomics3/peak_called/blacklist_rm/50_percent_called_peak/homer/CK_CTCF -size 200 #default


#EG
/projects/epigenomics3/epigenomics3_results/users/ajyzhu/Programs/Homer/bin/findMotifsGenome.pl /home/egibbard/epigenomics3/peak_called/blacklist_rm/50_percent_called_peak/CR_Evan_CTCF.bl_rm_50.narrowPeak hg19 /home/egibbard/epigenomics3/peak_called/blacklist_rm/50_percent_called_peak/homer/EG_CTCF/ -size 200 #default

#CHIP
findMotifsGenome.pl /home/egibbard/epigenomics3/peak_called/blacklist_rm/50_percent_called_peak/ChIP_CTCF_w_Input.bl_rm_50.narrowPeak hg19 /home/egibbard/epigenomics3/peak_called/blacklist_rm/50_percent_called_peak/homer/CHIP

#Input
#NA