module load python/3.6.1; /oak/stanford/groups/akundaje/marinovg/programs/idr-2.0.4/bin/idr --samples Native_ChIP_CTCF_high_MNase.2x25mers.unique.FL20-75bp.merged.pseudoRep1.MACS-2.1.0.p1e-1_peaks.narrowPeak.sorted.gz Native_ChIP_CTCF_high_MNase.2x25mers.unique.FL20-75bp.merged.pseudoRep2.MACS-2.1.0.p1e-1_peaks.narrowPeak.sorted.gz --input-file-type narrowPeak --output-file Native_ChIP_CTCF_high_MNase.2x25mers.unique.FL20-75bp.pseudoreps.IDR --rank p.value --soft-idr-threshold 0.05 --plot --use-best-multisummit-IDR
module load python/3.6.1; /oak/stanford/groups/akundaje/marinovg/programs/idr-2.0.4/bin/idr --samples Native_ChIP_CTCF_low_MNase.2x25mers.unique.FL20-75bp.merged.pseudoRep1.MACS-2.1.0.p1e-1_peaks.narrowPeak.sorted.gz Native_ChIP_CTCF_low_MNase.2x25mers.unique.FL20-75bp.merged.pseudoRep2.MACS-2.1.0.p1e-1_peaks.narrowPeak.sorted.gz --input-file-type narrowPeak --output-file Native_ChIP_CTCF_low_MNase.2x25mers.unique.FL20-75bp.pseudoreps.IDR --rank p.value --soft-idr-threshold 0.05 --plot --use-best-multisummit-IDR
module load python/3.6.1; /oak/stanford/groups/akundaje/marinovg/programs/idr-2.0.4/bin/idr --samples Native_ChIP_CTCF_medium_MNase.2x25mers.unique.FL20-75bp.merged.pseudoRep1.MACS-2.1.0.p1e-1_peaks.narrowPeak.sorted.gz Native_ChIP_CTCF_medium_MNase.2x25mers.unique.FL20-75bp.merged.pseudoRep2.MACS-2.1.0.p1e-1_peaks.narrowPeak.sorted.gz --input-file-type narrowPeak --output-file Native_ChIP_CTCF_medium_MNase.2x25mers.unique.FL20-75bp.pseudoreps.IDR --rank p.value --soft-idr-threshold 0.05 --plot --use-best-multisummit-IDR
module load python/3.6.1; /oak/stanford/groups/akundaje/marinovg/programs/idr-2.0.4/bin/idr --samples Native_ChIP_CTCF_high_MNase_1.2x25mers.unique.FL20-75bp.MACS-2.1.0.p1e-1_peaks.narrowPeak.sorted.gz Native_ChIP_CTCF_high_MNase_2.2x25mers.unique.FL20-75bp.MACS-2.1.0.p1e-1_peaks.narrowPeak.sorted.gz --input-file-type narrowPeak --output-file Native_ChIP_CTCF_high_MNase_1.2x25mers.unique.FL20-75bp.indreps.IDR --rank p.value --soft-idr-threshold 0.05 --plot --use-best-multisummit-IDR
module load python/3.6.1; /oak/stanford/groups/akundaje/marinovg/programs/idr-2.0.4/bin/idr --samples Native_ChIP_CTCF_low_MNase_1.2x25mers.unique.FL20-75bp.MACS-2.1.0.p1e-1_peaks.narrowPeak.sorted.gz Native_ChIP_CTCF_low_MNase_2.2x25mers.unique.FL20-75bp.MACS-2.1.0.p1e-1_peaks.narrowPeak.sorted.gz --input-file-type narrowPeak --output-file Native_ChIP_CTCF_low_MNase_1.2x25mers.unique.FL20-75bp.indreps.IDR --rank p.value --soft-idr-threshold 0.05 --plot --use-best-multisummit-IDR
module load python/3.6.1; /oak/stanford/groups/akundaje/marinovg/programs/idr-2.0.4/bin/idr --samples Native_ChIP_CTCF_medium_MNase_1.2x25mers.unique.FL20-75bp.MACS-2.1.0.p1e-1_peaks.narrowPeak.sorted.gz Native_ChIP_CTCF_medium_MNase_2.2x25mers.unique.FL20-75bp.MACS-2.1.0.p1e-1_peaks.narrowPeak.sorted.gz --input-file-type narrowPeak --output-file Native_ChIP_CTCF_medium_MNase_1.2x25mers.unique.FL20-75bp.indreps.IDR --rank p.value --soft-idr-threshold 0.05 --plot --use-best-multisummit-IDR
module load python/3.6.1; /oak/stanford/groups/akundaje/marinovg/programs/idr-2.0.4/bin/idr --samples Native_ChIP_CTCF_high_MNase.2x25mers.unique.merged.pseudoRep1.MACS-2.1.0.p1e-1_peaks.narrowPeak.sorted.gz Native_ChIP_CTCF_high_MNase.2x25mers.unique.merged.pseudoRep2.MACS-2.1.0.p1e-1_peaks.narrowPeak.sorted.gz --input-file-type narrowPeak --output-file Native_ChIP_CTCF_high_MNase.2x25mers.unique.pseudoreps.IDR --rank p.value --soft-idr-threshold 0.05 --plot --use-best-multisummit-IDR
module load python/3.6.1; /oak/stanford/groups/akundaje/marinovg/programs/idr-2.0.4/bin/idr --samples Native_ChIP_CTCF_low_MNase.2x25mers.unique.merged.pseudoRep1.MACS-2.1.0.p1e-1_peaks.narrowPeak.sorted.gz Native_ChIP_CTCF_low_MNase.2x25mers.unique.merged.pseudoRep2.MACS-2.1.0.p1e-1_peaks.narrowPeak.sorted.gz --input-file-type narrowPeak --output-file Native_ChIP_CTCF_low_MNase.2x25mers.unique.pseudoreps.IDR --rank p.value --soft-idr-threshold 0.05 --plot --use-best-multisummit-IDR
module load python/3.6.1; /oak/stanford/groups/akundaje/marinovg/programs/idr-2.0.4/bin/idr --samples Native_ChIP_CTCF_medium_MNase.2x25mers.unique.merged.pseudoRep1.MACS-2.1.0.p1e-1_peaks.narrowPeak.sorted.gz Native_ChIP_CTCF_medium_MNase.2x25mers.unique.merged.pseudoRep2.MACS-2.1.0.p1e-1_peaks.narrowPeak.sorted.gz --input-file-type narrowPeak --output-file Native_ChIP_CTCF_medium_MNase.2x25mers.unique.pseudoreps.IDR --rank p.value --soft-idr-threshold 0.05 --plot --use-best-multisummit-IDR
module load python/3.6.1; /oak/stanford/groups/akundaje/marinovg/programs/idr-2.0.4/bin/idr --samples Native_ChIP_CTCF_high_MNase_1.2x25mers.unique.MACS-2.1.0.p1e-1_peaks.narrowPeak.sorted.gz Native_ChIP_CTCF_high_MNase_2.2x25mers.unique.MACS-2.1.0.p1e-1_peaks.narrowPeak.sorted.gz --input-file-type narrowPeak --output-file Native_ChIP_CTCF_high_MNase_1.2x25mers.unique.indreps.IDR --rank p.value --soft-idr-threshold 0.05 --plot --use-best-multisummit-IDR
module load python/3.6.1; /oak/stanford/groups/akundaje/marinovg/programs/idr-2.0.4/bin/idr --samples Native_ChIP_CTCF_low_MNase_1.2x25mers.unique.MACS-2.1.0.p1e-1_peaks.narrowPeak.sorted.gz Native_ChIP_CTCF_low_MNase_2.2x25mers.unique.MACS-2.1.0.p1e-1_peaks.narrowPeak.sorted.gz --input-file-type narrowPeak --output-file Native_ChIP_CTCF_low_MNase_1.2x25mers.unique.indreps.IDR --rank p.value --soft-idr-threshold 0.05 --plot --use-best-multisummit-IDR
module load python/3.6.1; /oak/stanford/groups/akundaje/marinovg/programs/idr-2.0.4/bin/idr --samples Native_ChIP_CTCF_medium_MNase_1.2x25mers.unique.MACS-2.1.0.p1e-1_peaks.narrowPeak.sorted.gz Native_ChIP_CTCF_medium_MNase_2.2x25mers.unique.MACS-2.1.0.p1e-1_peaks.narrowPeak.sorted.gz --input-file-type narrowPeak --output-file Native_ChIP_CTCF_medium_MNase_1.2x25mers.unique.indreps.IDR --rank p.value --soft-idr-threshold 0.05 --plot --use-best-multisummit-IDR