/oak/stanford/groups/akundaje/marinovg/programs/MACS-2.1.0/bin/macs2 callpeak -t Native_ChIP_CTCF_high_MNase.2x25mers.unique.FL20-75bp.merged.bam -c Native_Input_high_MNase_20151207_PS_Hs_Input_C_ss-GSM2247158.2x25mers.unique.FL20-75bp.bam -n Native_ChIP_CTCF_high_MNase.2x25mers.unique.FL20-75bp.merged.MACS-2.1.0.p1e-1 -g hs -f BAM --to-large -p 1e-1 --keep-dup all
/oak/stanford/groups/akundaje/marinovg/programs/MACS-2.1.0/bin/macs2 callpeak -t Native_ChIP_CTCF_high_MNase.2x25mers.unique.FL20-75bp.merged.pseudoRep1.bam -c Native_Input_high_MNase_20151207_PS_Hs_Input_C_ss-GSM2247158.2x25mers.unique.FL20-75bp.pseudoRep1.bam -n Native_ChIP_CTCF_high_MNase.2x25mers.unique.FL20-75bp.merged.pseudoRep1.MACS-2.1.0.p1e-1 -g hs -f BAM --to-large -p 1e-1 --keep-dup all
/oak/stanford/groups/akundaje/marinovg/programs/MACS-2.1.0/bin/macs2 callpeak -t Native_ChIP_CTCF_high_MNase.2x25mers.unique.FL20-75bp.merged.pseudoRep2.bam -c Native_Input_high_MNase_20151207_PS_Hs_Input_C_ss-GSM2247158.2x25mers.unique.FL20-75bp.pseudoRep2.bam -n Native_ChIP_CTCF_high_MNase.2x25mers.unique.FL20-75bp.merged.pseudoRep2.MACS-2.1.0.p1e-1 -g hs -f BAM --to-large -p 1e-1 --keep-dup all
/oak/stanford/groups/akundaje/marinovg/programs/MACS-2.1.0/bin/macs2 callpeak -t Native_ChIP_CTCF_high_MNase.2x25mers.unique.merged.bam -c Native_Input_high_MNase_20151207_PS_Hs_Input_C_ss-GSM2247158.2x25mers.unique.bam -n Native_ChIP_CTCF_high_MNase.2x25mers.unique.merged.MACS-2.1.0.p1e-1 -g hs -f BAM --to-large -p 1e-1 --keep-dup all
/oak/stanford/groups/akundaje/marinovg/programs/MACS-2.1.0/bin/macs2 callpeak -t Native_ChIP_CTCF_high_MNase.2x25mers.unique.merged.pseudoRep1.bam -c Native_Input_high_MNase_20151207_PS_Hs_Input_C_ss-GSM2247158.2x25mers.unique.pseudoRep1.bam -n Native_ChIP_CTCF_high_MNase.2x25mers.unique.merged.pseudoRep1.MACS-2.1.0.p1e-1 -g hs -f BAM --to-large -p 1e-1 --keep-dup all
/oak/stanford/groups/akundaje/marinovg/programs/MACS-2.1.0/bin/macs2 callpeak -t Native_ChIP_CTCF_high_MNase.2x25mers.unique.merged.pseudoRep2.bam -c Native_Input_high_MNase_20151207_PS_Hs_Input_C_ss-GSM2247158.2x25mers.unique.pseudoRep2.bam -n Native_ChIP_CTCF_high_MNase.2x25mers.unique.merged.pseudoRep2.MACS-2.1.0.p1e-1 -g hs -f BAM --to-large -p 1e-1 --keep-dup all
/oak/stanford/groups/akundaje/marinovg/programs/MACS-2.1.0/bin/macs2 callpeak -t Native_ChIP_CTCF_low_MNase.2x25mers.unique.FL20-75bp.merged.bam -c Native_Input_low_MNase_20151207_PS_Hs_Input_E_ss-GSM2247156.2x25mers.unique.FL20-75bp.bam -n Native_ChIP_CTCF_low_MNase.2x25mers.unique.FL20-75bp.merged.MACS-2.1.0.p1e-1 -g hs -f BAM --to-large -p 1e-1 --keep-dup all
/oak/stanford/groups/akundaje/marinovg/programs/MACS-2.1.0/bin/macs2 callpeak -t Native_ChIP_CTCF_low_MNase.2x25mers.unique.FL20-75bp.merged.pseudoRep1.bam -c Native_Input_low_MNase_20151207_PS_Hs_Input_E_ss-GSM2247156.2x25mers.unique.FL20-75bp.pseudoRep1.bam -n Native_ChIP_CTCF_low_MNase.2x25mers.unique.FL20-75bp.merged.pseudoRep1.MACS-2.1.0.p1e-1 -g hs -f BAM --to-large -p 1e-1 --keep-dup all
/oak/stanford/groups/akundaje/marinovg/programs/MACS-2.1.0/bin/macs2 callpeak -t Native_ChIP_CTCF_low_MNase.2x25mers.unique.FL20-75bp.merged.pseudoRep2.bam -c Native_Input_low_MNase_20151207_PS_Hs_Input_E_ss-GSM2247156.2x25mers.unique.FL20-75bp.pseudoRep2.bam -n Native_ChIP_CTCF_low_MNase.2x25mers.unique.FL20-75bp.merged.pseudoRep2.MACS-2.1.0.p1e-1 -g hs -f BAM --to-large -p 1e-1 --keep-dup all
/oak/stanford/groups/akundaje/marinovg/programs/MACS-2.1.0/bin/macs2 callpeak -t Native_ChIP_CTCF_low_MNase.2x25mers.unique.merged.bam -c Native_Input_low_MNase_20151207_PS_Hs_Input_E_ss-GSM2247156.2x25mers.unique.bam -n Native_ChIP_CTCF_low_MNase.2x25mers.unique.merged.MACS-2.1.0.p1e-1 -g hs -f BAM --to-large -p 1e-1 --keep-dup all
/oak/stanford/groups/akundaje/marinovg/programs/MACS-2.1.0/bin/macs2 callpeak -t Native_ChIP_CTCF_low_MNase.2x25mers.unique.merged.pseudoRep1.bam -c Native_Input_low_MNase_20151207_PS_Hs_Input_E_ss-GSM2247156.2x25mers.unique.pseudoRep1.bam -n Native_ChIP_CTCF_low_MNase.2x25mers.unique.merged.pseudoRep1.MACS-2.1.0.p1e-1 -g hs -f BAM --to-large -p 1e-1 --keep-dup all
/oak/stanford/groups/akundaje/marinovg/programs/MACS-2.1.0/bin/macs2 callpeak -t Native_ChIP_CTCF_low_MNase.2x25mers.unique.merged.pseudoRep2.bam -c Native_Input_low_MNase_20151207_PS_Hs_Input_E_ss-GSM2247156.2x25mers.unique.pseudoRep2.bam -n Native_ChIP_CTCF_low_MNase.2x25mers.unique.merged.pseudoRep2.MACS-2.1.0.p1e-1 -g hs -f BAM --to-large -p 1e-1 --keep-dup all
/oak/stanford/groups/akundaje/marinovg/programs/MACS-2.1.0/bin/macs2 callpeak -t Native_ChIP_CTCF_medium_MNase.2x25mers.unique.FL20-75bp.merged.bam -c Native_Input_medium_MNase_20151207_PS_Hs_Input_D_ss-GSM2247157.2x25mers.unique.FL20-75bp.bam -n Native_ChIP_CTCF_medium_MNase.2x25mers.unique.FL20-75bp.merged.MACS-2.1.0.p1e-1 -g hs -f BAM --to-large -p 1e-1 --keep-dup all
/oak/stanford/groups/akundaje/marinovg/programs/MACS-2.1.0/bin/macs2 callpeak -t Native_ChIP_CTCF_medium_MNase.2x25mers.unique.FL20-75bp.merged.pseudoRep1.bam -c Native_Input_medium_MNase_20151207_PS_Hs_Input_D_ss-GSM2247157.2x25mers.unique.FL20-75bp.pseudoRep1.bam -n Native_ChIP_CTCF_medium_MNase.2x25mers.unique.FL20-75bp.merged.pseudoRep1.MACS-2.1.0.p1e-1 -g hs -f BAM --to-large -p 1e-1 --keep-dup all
/oak/stanford/groups/akundaje/marinovg/programs/MACS-2.1.0/bin/macs2 callpeak -t Native_ChIP_CTCF_medium_MNase.2x25mers.unique.FL20-75bp.merged.pseudoRep2.bam -c Native_Input_medium_MNase_20151207_PS_Hs_Input_D_ss-GSM2247157.2x25mers.unique.FL20-75bp.pseudoRep2.bam -n Native_ChIP_CTCF_medium_MNase.2x25mers.unique.FL20-75bp.merged.pseudoRep2.MACS-2.1.0.p1e-1 -g hs -f BAM --to-large -p 1e-1 --keep-dup all
/oak/stanford/groups/akundaje/marinovg/programs/MACS-2.1.0/bin/macs2 callpeak -t Native_ChIP_CTCF_medium_MNase.2x25mers.unique.merged.bam -c Native_Input_medium_MNase_20151207_PS_Hs_Input_D_ss-GSM2247157.2x25mers.unique.bam -n Native_ChIP_CTCF_medium_MNase.2x25mers.unique.merged.MACS-2.1.0.p1e-1 -g hs -f BAM --to-large -p 1e-1 --keep-dup all
/oak/stanford/groups/akundaje/marinovg/programs/MACS-2.1.0/bin/macs2 callpeak -t Native_ChIP_CTCF_medium_MNase.2x25mers.unique.merged.pseudoRep1.bam -c Native_Input_medium_MNase_20151207_PS_Hs_Input_D_ss-GSM2247157.2x25mers.unique.pseudoRep1.bam -n Native_ChIP_CTCF_medium_MNase.2x25mers.unique.merged.pseudoRep1.MACS-2.1.0.p1e-1 -g hs -f BAM --to-large -p 1e-1 --keep-dup all
/oak/stanford/groups/akundaje/marinovg/programs/MACS-2.1.0/bin/macs2 callpeak -t Native_ChIP_CTCF_medium_MNase.2x25mers.unique.merged.pseudoRep2.bam -c Native_Input_medium_MNase_20151207_PS_Hs_Input_D_ss-GSM2247157.2x25mers.unique.pseudoRep2.bam -n Native_ChIP_CTCF_medium_MNase.2x25mers.unique.merged.pseudoRep2.MACS-2.1.0.p1e-1 -g hs -f BAM --to-large -p 1e-1 --keep-dup all
/oak/stanford/groups/akundaje/marinovg/programs/MACS-2.1.0/bin/macs2 callpeak -t /oak/stanford/groups/akundaje/marinovg/ENCODE4/CRISPR/datasets-CUTnRUN/Native_ChIP_CTCF_high_MNase_1_20150925_PS_Hs_N_CTCF_C-GSM2247154/Native_ChIP_CTCF_high_MNase_1_20150925_PS_Hs_N_CTCF_C-GSM2247154.2x25mers.unique.FL20-75bp.bam -c /oak/stanford/groups/akundaje/marinovg/ENCODE4/CRISPR/datasets-CUTnRUN/Native_Input_high_MNase_20151207_PS_Hs_Input_C_ss-GSM2247158/Native_Input_high_MNase_20151207_PS_Hs_Input_C_ss-GSM2247158.2x25mers.unique.FL20-75bp.bam -n Native_ChIP_CTCF_high_MNase_1.2x25mers.unique.FL20-75bp.MACS-2.1.0.p1e-1 -g hs -f BAM --to-large -p 1e-1 --keep-dup all
/oak/stanford/groups/akundaje/marinovg/programs/MACS-2.1.0/bin/macs2 callpeak -t /oak/stanford/groups/akundaje/marinovg/ENCODE4/CRISPR/datasets-CUTnRUN/Native_ChIP_CTCF_high_MNase_2_20151104_PS_Hs_N_CTCF_C-GSM2247155/Native_ChIP_CTCF_high_MNase_2_20151104_PS_Hs_N_CTCF_C-GSM2247155.2x25mers.unique.FL20-75bp.bam -c /oak/stanford/groups/akundaje/marinovg/ENCODE4/CRISPR/datasets-CUTnRUN/Native_Input_high_MNase_20151207_PS_Hs_Input_C_ss-GSM2247158/Native_Input_high_MNase_20151207_PS_Hs_Input_C_ss-GSM2247158.2x25mers.unique.FL20-75bp.bam -n Native_ChIP_CTCF_high_MNase_2.2x25mers.unique.FL20-75bp.MACS-2.1.0.p1e-1 -g hs -f BAM --to-large -p 1e-1 --keep-dup all
/oak/stanford/groups/akundaje/marinovg/programs/MACS-2.1.0/bin/macs2 callpeak -t /oak/stanford/groups/akundaje/marinovg/ENCODE4/CRISPR/datasets-CUTnRUN/Native_ChIP_CTCF_low_MNase_1_20150925_PS_Hs_N_CTCF_E-GSM2247150/Native_ChIP_CTCF_low_MNase_1_20150925_PS_Hs_N_CTCF_E-GSM2247150.2x25mers.unique.FL20-75bp.bam -c /oak/stanford/groups/akundaje/marinovg/ENCODE4/CRISPR/datasets-CUTnRUN/Native_Input_low_MNase_20151207_PS_Hs_Input_E_ss-GSM2247156/Native_Input_low_MNase_20151207_PS_Hs_Input_E_ss-GSM2247156.2x25mers.unique.FL20-75bp.bam -n Native_ChIP_CTCF_low_MNase_1.2x25mers.unique.FL20-75bp.MACS-2.1.0.p1e-1 -g hs -f BAM --to-large -p 1e-1 --keep-dup all
/oak/stanford/groups/akundaje/marinovg/programs/MACS-2.1.0/bin/macs2 callpeak -t /oak/stanford/groups/akundaje/marinovg/ENCODE4/CRISPR/datasets-CUTnRUN/Native_ChIP_CTCF_low_MNase_2_20151104_PS_Hs_N_CTCF_E-GSM2247151/Native_ChIP_CTCF_low_MNase_2_20151104_PS_Hs_N_CTCF_E-GSM2247151.2x25mers.unique.FL20-75bp.bam -c /oak/stanford/groups/akundaje/marinovg/ENCODE4/CRISPR/datasets-CUTnRUN/Native_Input_low_MNase_20151207_PS_Hs_Input_E_ss-GSM2247156/Native_Input_low_MNase_20151207_PS_Hs_Input_E_ss-GSM2247156.2x25mers.unique.FL20-75bp.bam -n Native_ChIP_CTCF_low_MNase_2.2x25mers.unique.FL20-75bp.MACS-2.1.0.p1e-1 -g hs -f BAM --to-large -p 1e-1 --keep-dup all
/oak/stanford/groups/akundaje/marinovg/programs/MACS-2.1.0/bin/macs2 callpeak -t /oak/stanford/groups/akundaje/marinovg/ENCODE4/CRISPR/datasets-CUTnRUN/Native_ChIP_CTCF_medium_MNase_1_20150925_PS_Hs_N_CTCF_D-GSM2247152/Native_ChIP_CTCF_medium_MNase_1_20150925_PS_Hs_N_CTCF_D-GSM2247152.2x25mers.unique.FL20-75bp.bam -c /oak/stanford/groups/akundaje/marinovg/ENCODE4/CRISPR/datasets-CUTnRUN/Native_Input_medium_MNase_20151207_PS_Hs_Input_D_ss-GSM2247157/Native_Input_medium_MNase_20151207_PS_Hs_Input_D_ss-GSM2247157.2x25mers.unique.FL20-75bp.bam -n Native_ChIP_CTCF_medium_MNase_1.2x25mers.unique.FL20-75bp.MACS-2.1.0.p1e-1 -g hs -f BAM --to-large -p 1e-1 --keep-dup all
/oak/stanford/groups/akundaje/marinovg/programs/MACS-2.1.0/bin/macs2 callpeak -t /oak/stanford/groups/akundaje/marinovg/ENCODE4/CRISPR/datasets-CUTnRUN/Native_ChIP_CTCF_medium_MNase_2_20151104_PS_Hs_N_CTCF_D-GSM2247153/Native_ChIP_CTCF_medium_MNase_2_20151104_PS_Hs_N_CTCF_D-GSM2247153.2x25mers.unique.FL20-75bp.bam -c /oak/stanford/groups/akundaje/marinovg/ENCODE4/CRISPR/datasets-CUTnRUN/Native_Input_medium_MNase_20151207_PS_Hs_Input_D_ss-GSM2247157/Native_Input_medium_MNase_20151207_PS_Hs_Input_D_ss-GSM2247157.2x25mers.unique.FL20-75bp.bam -n Native_ChIP_CTCF_medium_MNase_2.2x25mers.unique.FL20-75bp.MACS-2.1.0.p1e-1 -g hs -f BAM --to-large -p 1e-1 --keep-dup all
/oak/stanford/groups/akundaje/marinovg/programs/MACS-2.1.0/bin/macs2 callpeak -t /oak/stanford/groups/akundaje/marinovg/ENCODE4/CRISPR/datasets-CUTnRUN/Native_ChIP_CTCF_high_MNase_1_20150925_PS_Hs_N_CTCF_C-GSM2247154/Native_ChIP_CTCF_high_MNase_1_20150925_PS_Hs_N_CTCF_C-GSM2247154.2x25mers.unique.bam -c /oak/stanford/groups/akundaje/marinovg/ENCODE4/CRISPR/datasets-CUTnRUN/Native_Input_high_MNase_20151207_PS_Hs_Input_C_ss-GSM2247158/Native_Input_high_MNase_20151207_PS_Hs_Input_C_ss-GSM2247158.2x25mers.unique.bam -n Native_ChIP_CTCF_high_MNase_1.2x25mers.unique.MACS-2.1.0.p1e-1 -g hs -f BAM --to-large -p 1e-1 --keep-dup all
/oak/stanford/groups/akundaje/marinovg/programs/MACS-2.1.0/bin/macs2 callpeak -t /oak/stanford/groups/akundaje/marinovg/ENCODE4/CRISPR/datasets-CUTnRUN/Native_ChIP_CTCF_high_MNase_2_20151104_PS_Hs_N_CTCF_C-GSM2247155/Native_ChIP_CTCF_high_MNase_2_20151104_PS_Hs_N_CTCF_C-GSM2247155.2x25mers.unique.bam -c /oak/stanford/groups/akundaje/marinovg/ENCODE4/CRISPR/datasets-CUTnRUN/Native_Input_high_MNase_20151207_PS_Hs_Input_C_ss-GSM2247158/Native_Input_high_MNase_20151207_PS_Hs_Input_C_ss-GSM2247158.2x25mers.unique.bam -n Native_ChIP_CTCF_high_MNase_2.2x25mers.unique.MACS-2.1.0.p1e-1 -g hs -f BAM --to-large -p 1e-1 --keep-dup all
/oak/stanford/groups/akundaje/marinovg/programs/MACS-2.1.0/bin/macs2 callpeak -t /oak/stanford/groups/akundaje/marinovg/ENCODE4/CRISPR/datasets-CUTnRUN/Native_ChIP_CTCF_low_MNase_1_20150925_PS_Hs_N_CTCF_E-GSM2247150/Native_ChIP_CTCF_low_MNase_1_20150925_PS_Hs_N_CTCF_E-GSM2247150.2x25mers.unique.bam -c /oak/stanford/groups/akundaje/marinovg/ENCODE4/CRISPR/datasets-CUTnRUN/Native_Input_low_MNase_20151207_PS_Hs_Input_E_ss-GSM2247156/Native_Input_low_MNase_20151207_PS_Hs_Input_E_ss-GSM2247156.2x25mers.unique.bam -n Native_ChIP_CTCF_low_MNase_1.2x25mers.unique.MACS-2.1.0.p1e-1 -g hs -f BAM --to-large -p 1e-1 --keep-dup all
/oak/stanford/groups/akundaje/marinovg/programs/MACS-2.1.0/bin/macs2 callpeak -t /oak/stanford/groups/akundaje/marinovg/ENCODE4/CRISPR/datasets-CUTnRUN/Native_ChIP_CTCF_low_MNase_2_20151104_PS_Hs_N_CTCF_E-GSM2247151/Native_ChIP_CTCF_low_MNase_2_20151104_PS_Hs_N_CTCF_E-GSM2247151.2x25mers.unique.bam -c /oak/stanford/groups/akundaje/marinovg/ENCODE4/CRISPR/datasets-CUTnRUN/Native_Input_low_MNase_20151207_PS_Hs_Input_E_ss-GSM2247156/Native_Input_low_MNase_20151207_PS_Hs_Input_E_ss-GSM2247156.2x25mers.unique.bam -n Native_ChIP_CTCF_low_MNase_2.2x25mers.unique.MACS-2.1.0.p1e-1 -g hs -f BAM --to-large -p 1e-1 --keep-dup all
/oak/stanford/groups/akundaje/marinovg/programs/MACS-2.1.0/bin/macs2 callpeak -t /oak/stanford/groups/akundaje/marinovg/ENCODE4/CRISPR/datasets-CUTnRUN/Native_ChIP_CTCF_medium_MNase_1_20150925_PS_Hs_N_CTCF_D-GSM2247152/Native_ChIP_CTCF_medium_MNase_1_20150925_PS_Hs_N_CTCF_D-GSM2247152.2x25mers.unique.bam -c /oak/stanford/groups/akundaje/marinovg/ENCODE4/CRISPR/datasets-CUTnRUN/Native_Input_medium_MNase_20151207_PS_Hs_Input_D_ss-GSM2247157/Native_Input_medium_MNase_20151207_PS_Hs_Input_D_ss-GSM2247157.2x25mers.unique.bam -n Native_ChIP_CTCF_medium_MNase_1.2x25mers.unique.MACS-2.1.0.p1e-1 -g hs -f BAM --to-large -p 1e-1 --keep-dup all
/oak/stanford/groups/akundaje/marinovg/programs/MACS-2.1.0/bin/macs2 callpeak -t /oak/stanford/groups/akundaje/marinovg/ENCODE4/CRISPR/datasets-CUTnRUN/Native_ChIP_CTCF_medium_MNase_2_20151104_PS_Hs_N_CTCF_D-GSM2247153/Native_ChIP_CTCF_medium_MNase_2_20151104_PS_Hs_N_CTCF_D-GSM2247153.2x25mers.unique.bam -c /oak/stanford/groups/akundaje/marinovg/ENCODE4/CRISPR/datasets-CUTnRUN/Native_Input_medium_MNase_20151207_PS_Hs_Input_D_ss-GSM2247157/Native_Input_medium_MNase_20151207_PS_Hs_Input_D_ss-GSM2247157.2x25mers.unique.bam -n Native_ChIP_CTCF_medium_MNase_2.2x25mers.unique.MACS-2.1.0.p1e-1 -g hs -f BAM --to-large -p 1e-1 --keep-dup all