module load python/3.6.1; /oak/stanford/groups/akundaje/marinovg/programs/idr-2.0.4/bin/idr --samples BELT/BELT-CTCF-GM12878-Rep1.relaxed.narrowPeak.top300K.gz BELT/BELT-CTCF-GM12878-Rep2.relaxed.narrowPeak.top300K.gz --input-file-type narrowPeak --output-file BELT/BELT-CTCF-GM12878-IDR2 --peak-list BELT/BELT-CTCF-GM12878-Rep0.relaxed.narrowPeak.top300K.gz --rank signal.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 BELT/BELT-GABP-GM12878-Rep1.relaxed.narrowPeak.top300K.gz BELT/BELT-GABP-GM12878-Rep2.relaxed.narrowPeak.top300K.gz --input-file-type narrowPeak --output-file BELT/BELT-GABP-GM12878-IDR2 --peak-list BELT/BELT-GABP-GM12878-Rep0.relaxed.narrowPeak.top300K.gz --rank signal.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 BELT/BELT-GABP-HELAS3-Rep1.relaxed.narrowPeak.top300K.gz BELT/BELT-GABP-HELAS3-Rep2.relaxed.narrowPeak.top300K.gz --input-file-type narrowPeak --output-file BELT/BELT-GABP-HELAS3-IDR2 --peak-list BELT/BELT-GABP-HELAS3-Rep0.relaxed.narrowPeak.top300K.gz --rank signal.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 BELT/BELT-P300-K562-Rep1.relaxed.narrowPeak.top300K.gz BELT/BELT-P300-K562-Rep2.relaxed.narrowPeak.top300K.gz --input-file-type narrowPeak --output-file BELT/BELT-P300-K562-IDR2 --peak-list BELT/BELT-P300-K562-Rep0.relaxed.narrowPeak.top300K.gz --rank signal.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 BELT/BELT-POL2-H1ESC-Rep1.relaxed.narrowPeak.top300K.gz BELT/BELT-POL2-H1ESC-Rep2.relaxed.narrowPeak.top300K.gz --input-file-type narrowPeak --output-file BELT/BELT-POL2-H1ESC-IDR2 --peak-list BELT/BELT-POL2-H1ESC-Rep0.relaxed.narrowPeak.top300K.gz --rank signal.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 BELT/BELT-POL2-H1NEURON-Rep1.relaxed.narrowPeak.top300K.gz BELT/BELT-POL2-H1NEURON-Rep2.relaxed.narrowPeak.top300K.gz --input-file-type narrowPeak --output-file BELT/BELT-POL2-H1NEURON-IDR2 --peak-list BELT/BELT-POL2-H1NEURON-Rep0.relaxed.narrowPeak.top300K.gz --rank signal.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 BELT/BELT-ZNF274-K562-Rep1.relaxed.narrowPeak.top300K.gz BELT/BELT-ZNF274-K562-Rep2.relaxed.narrowPeak.top300K.gz --input-file-type narrowPeak --output-file BELT/BELT-ZNF274-K562-IDR2 --peak-list BELT/BELT-ZNF274-K562-Rep0.relaxed.narrowPeak.top300K.gz --rank signal.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 dPeak3/dPeak3-CTCF-GM12878-Rep1.relaxed.narrowPeak.top300K.gz dPeak3/dPeak3-CTCF-GM12878-Rep2.relaxed.narrowPeak.top300K.gz --input-file-type narrowPeak --output-file dPeak3/dPeak3-CTCF-GM12878-IDR2 --peak-list dPeak3/dPeak3-CTCF-GM12878-Rep0.relaxed.narrowPeak.top300K.gz --rank signal.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 dPeak3/dPeak3-GABP-GM12878-Rep1.relaxed.narrowPeak.top300K.gz dPeak3/dPeak3-GABP-GM12878-Rep2.relaxed.narrowPeak.top300K.gz --input-file-type narrowPeak --output-file dPeak3/dPeak3-GABP-GM12878-IDR2 --peak-list dPeak3/dPeak3-GABP-GM12878-Rep0.relaxed.narrowPeak.top300K.gz --rank signal.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 dPeak3/dPeak3-GABP-HELAS3-Rep1.relaxed.narrowPeak.top300K.gz dPeak3/dPeak3-GABP-HELAS3-Rep2.relaxed.narrowPeak.top300K.gz --input-file-type narrowPeak --output-file dPeak3/dPeak3-GABP-HELAS3-IDR2 --peak-list dPeak3/dPeak3-GABP-HELAS3-Rep0.relaxed.narrowPeak.top300K.gz --rank signal.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 dPeak3/dPeak3-P300-K562-Rep1.relaxed.narrowPeak.top300K.gz dPeak3/dPeak3-P300-K562-Rep2.relaxed.narrowPeak.top300K.gz --input-file-type narrowPeak --output-file dPeak3/dPeak3-P300-K562-IDR2 --peak-list dPeak3/dPeak3-P300-K562-Rep0.relaxed.narrowPeak.top300K.gz --rank signal.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 dPeak3/dPeak3-POL2-H1ESC-Rep1.relaxed.narrowPeak.top300K.gz dPeak3/dPeak3-POL2-H1ESC-Rep2.relaxed.narrowPeak.top300K.gz --input-file-type narrowPeak --output-file dPeak3/dPeak3-POL2-H1ESC-IDR2 --peak-list dPeak3/dPeak3-POL2-H1ESC-Rep0.relaxed.narrowPeak.top300K.gz --rank signal.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 dPeak3/dPeak3-POL2-H1NEURON-Rep1.relaxed.narrowPeak.top300K.gz dPeak3/dPeak3-POL2-H1NEURON-Rep2.relaxed.narrowPeak.top300K.gz --input-file-type narrowPeak --output-file dPeak3/dPeak3-POL2-H1NEURON-IDR2 --peak-list dPeak3/dPeak3-POL2-H1NEURON-Rep0.relaxed.narrowPeak.top300K.gz --rank signal.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 dPeak3/dPeak3-ZNF274-K562-Rep1.relaxed.narrowPeak.top300K.gz dPeak3/dPeak3-ZNF274-K562-Rep2.relaxed.narrowPeak.top300K.gz --input-file-type narrowPeak --output-file dPeak3/dPeak3-ZNF274-K562-IDR2 --peak-list dPeak3/dPeak3-ZNF274-K562-Rep0.relaxed.narrowPeak.top300K.gz --rank signal.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 GEMv2/GEMv2-CTCF-GM12878-Rep1.relaxed.narrowPeak.top300K.gz GEMv2/GEMv2-CTCF-GM12878-Rep2.relaxed.narrowPeak.top300K.gz --input-file-type narrowPeak --output-file GEMv2/GEMv2-CTCF-GM12878-IDR2 --peak-list GEMv2/GEMv2-CTCF-GM12878-Rep0.relaxed.narrowPeak.top300K.gz --rank signal.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 GEMv2/GEMv2-GABP-GM12878-Rep1.relaxed.narrowPeak.top300K.gz GEMv2/GEMv2-GABP-GM12878-Rep2.relaxed.narrowPeak.top300K.gz --input-file-type narrowPeak --output-file GEMv2/GEMv2-GABP-GM12878-IDR2 --peak-list GEMv2/GEMv2-GABP-GM12878-Rep0.relaxed.narrowPeak.top300K.gz --rank signal.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 GEMv2/GEMv2-GABP-HELAS3-Rep1.relaxed.narrowPeak.top300K.gz GEMv2/GEMv2-GABP-HELAS3-Rep2.relaxed.narrowPeak.top300K.gz --input-file-type narrowPeak --output-file GEMv2/GEMv2-GABP-HELAS3-IDR2 --peak-list GEMv2/GEMv2-GABP-HELAS3-Rep0.relaxed.narrowPeak.top300K.gz --rank signal.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 GEMv2/GEMv2-P300-K562-Rep1.relaxed.narrowPeak.top300K.gz GEMv2/GEMv2-P300-K562-Rep2.relaxed.narrowPeak.top300K.gz --input-file-type narrowPeak --output-file GEMv2/GEMv2-P300-K562-IDR2 --peak-list GEMv2/GEMv2-P300-K562-Rep0.relaxed.narrowPeak.top300K.gz --rank signal.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 GEMv2/GEMv2-POL2-H1ESC-Rep1.relaxed.narrowPeak.top300K.gz GEMv2/GEMv2-POL2-H1ESC-Rep2.relaxed.narrowPeak.top300K.gz --input-file-type narrowPeak --output-file GEMv2/GEMv2-POL2-H1ESC-IDR2 --peak-list GEMv2/GEMv2-POL2-H1ESC-Rep0.relaxed.narrowPeak.top300K.gz --rank signal.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 GEMv2/GEMv2-POL2-H1NEURON-Rep1.relaxed.narrowPeak.top300K.gz GEMv2/GEMv2-POL2-H1NEURON-Rep2.relaxed.narrowPeak.top300K.gz --input-file-type narrowPeak --output-file GEMv2/GEMv2-POL2-H1NEURON-IDR2 --peak-list GEMv2/GEMv2-POL2-H1NEURON-Rep0.relaxed.narrowPeak.top300K.gz --rank signal.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 GEMv2/GEMv2-ZNF274-K562-Rep1.relaxed.narrowPeak.top300K.gz GEMv2/GEMv2-ZNF274-K562-Rep2.relaxed.narrowPeak.top300K.gz --input-file-type narrowPeak --output-file GEMv2/GEMv2-ZNF274-K562-IDR2 --peak-list GEMv2/GEMv2-ZNF274-K562-Rep0.relaxed.narrowPeak.top300K.gz --rank signal.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 GPS/GPS-CTCF-GM12878-Rep1.relaxed.narrowPeak.top300K.gz GPS/GPS-CTCF-GM12878-Rep2.relaxed.narrowPeak.top300K.gz --input-file-type narrowPeak --output-file GPS/GPS-CTCF-GM12878-IDR2 --peak-list GPS/GPS-CTCF-GM12878-Rep0.relaxed.narrowPeak.top300K.gz --rank signal.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 GPS/GPS-GABP-GM12878-Rep1.relaxed.narrowPeak.top300K.gz GPS/GPS-GABP-GM12878-Rep2.relaxed.narrowPeak.top300K.gz --input-file-type narrowPeak --output-file GPS/GPS-GABP-GM12878-IDR2 --peak-list GPS/GPS-GABP-GM12878-Rep0.relaxed.narrowPeak.top300K.gz --rank signal.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 GPS/GPS-GABP-HELAS3-Rep1.relaxed.narrowPeak.top300K.gz GPS/GPS-GABP-HELAS3-Rep2.relaxed.narrowPeak.top300K.gz --input-file-type narrowPeak --output-file GPS/GPS-GABP-HELAS3-IDR2 --peak-list GPS/GPS-GABP-HELAS3-Rep0.relaxed.narrowPeak.top300K.gz --rank signal.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 GPS/GPS-P300-K562-Rep1.relaxed.narrowPeak.top300K.gz GPS/GPS-P300-K562-Rep2.relaxed.narrowPeak.top300K.gz --input-file-type narrowPeak --output-file GPS/GPS-P300-K562-IDR2 --peak-list GPS/GPS-P300-K562-Rep0.relaxed.narrowPeak.top300K.gz --rank signal.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 GPS/GPS-POL2-H1ESC-Rep1.relaxed.narrowPeak.top300K.gz GPS/GPS-POL2-H1ESC-Rep2.relaxed.narrowPeak.top300K.gz --input-file-type narrowPeak --output-file GPS/GPS-POL2-H1ESC-IDR2 --peak-list GPS/GPS-POL2-H1ESC-Rep0.relaxed.narrowPeak.top300K.gz --rank signal.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 GPS/GPS-POL2-H1NEURON-Rep1.relaxed.narrowPeak.top300K.gz GPS/GPS-POL2-H1NEURON-Rep2.relaxed.narrowPeak.top300K.gz --input-file-type narrowPeak --output-file GPS/GPS-POL2-H1NEURON-IDR2 --peak-list GPS/GPS-POL2-H1NEURON-Rep0.relaxed.narrowPeak.top300K.gz --rank signal.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 GPS/GPS-ZNF274-K562-Rep1.relaxed.narrowPeak.top300K.gz GPS/GPS-ZNF274-K562-Rep2.relaxed.narrowPeak.top300K.gz --input-file-type narrowPeak --output-file GPS/GPS-ZNF274-K562-IDR2 --peak-list GPS/GPS-ZNF274-K562-Rep0.relaxed.narrowPeak.top300K.gz --rank signal.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 GPSv2/GPSv2-CTCF-GM12878-Rep1.relaxed.narrowPeak.top300K.gz GPSv2/GPSv2-CTCF-GM12878-Rep2.relaxed.narrowPeak.top300K.gz --input-file-type narrowPeak --output-file GPSv2/GPSv2-CTCF-GM12878-IDR2 --peak-list GPSv2/GPSv2-CTCF-GM12878-Rep0.relaxed.narrowPeak.top300K.gz --rank signal.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 GPSv2/GPSv2-GABP-GM12878-Rep1.relaxed.narrowPeak.top300K.gz GPSv2/GPSv2-GABP-GM12878-Rep2.relaxed.narrowPeak.top300K.gz --input-file-type narrowPeak --output-file GPSv2/GPSv2-GABP-GM12878-IDR2 --peak-list GPSv2/GPSv2-GABP-GM12878-Rep0.relaxed.narrowPeak.top300K.gz --rank signal.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 GPSv2/GPSv2-GABP-HELAS3-Rep1.relaxed.narrowPeak.top300K.gz GPSv2/GPSv2-GABP-HELAS3-Rep2.relaxed.narrowPeak.top300K.gz --input-file-type narrowPeak --output-file GPSv2/GPSv2-GABP-HELAS3-IDR2 --peak-list GPSv2/GPSv2-GABP-HELAS3-Rep0.relaxed.narrowPeak.top300K.gz --rank signal.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 GPSv2/GPSv2-P300-K562-Rep1.relaxed.narrowPeak.top300K.gz GPSv2/GPSv2-P300-K562-Rep2.relaxed.narrowPeak.top300K.gz --input-file-type narrowPeak --output-file GPSv2/GPSv2-P300-K562-IDR2 --peak-list GPSv2/GPSv2-P300-K562-Rep0.relaxed.narrowPeak.top300K.gz --rank signal.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 GPSv2/GPSv2-POL2-H1ESC-Rep1.relaxed.narrowPeak.top300K.gz GPSv2/GPSv2-POL2-H1ESC-Rep2.relaxed.narrowPeak.top300K.gz --input-file-type narrowPeak --output-file GPSv2/GPSv2-POL2-H1ESC-IDR2 --peak-list GPSv2/GPSv2-POL2-H1ESC-Rep0.relaxed.narrowPeak.top300K.gz --rank signal.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 GPSv2/GPSv2-POL2-H1NEURON-Rep1.relaxed.narrowPeak.top300K.gz GPSv2/GPSv2-POL2-H1NEURON-Rep2.relaxed.narrowPeak.top300K.gz --input-file-type narrowPeak --output-file GPSv2/GPSv2-POL2-H1NEURON-IDR2 --peak-list GPSv2/GPSv2-POL2-H1NEURON-Rep0.relaxed.narrowPeak.top300K.gz --rank signal.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 GPSv2/GPSv2-ZNF274-K562-Rep1.relaxed.narrowPeak.top300K.gz GPSv2/GPSv2-ZNF274-K562-Rep2.relaxed.narrowPeak.top300K.gz --input-file-type narrowPeak --output-file GPSv2/GPSv2-ZNF274-K562-IDR2 --peak-list GPSv2/GPSv2-ZNF274-K562-Rep0.relaxed.narrowPeak.top300K.gz --rank signal.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 Hotspot/Hotspot-CTCF-GM12878-Rep1.relaxed.narrowPeak.top300K.gz Hotspot/Hotspot-CTCF-GM12878-Rep2.relaxed.narrowPeak.top300K.gz --input-file-type narrowPeak --output-file Hotspot/Hotspot-CTCF-GM12878-IDR2 --peak-list Hotspot/Hotspot-CTCF-GM12878-Rep0.relaxed.narrowPeak.top300K.gz --rank signal.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 Hotspot/Hotspot-GABP-GM12878-Rep1.relaxed.narrowPeak.top300K.gz Hotspot/Hotspot-GABP-GM12878-Rep2.relaxed.narrowPeak.top300K.gz --input-file-type narrowPeak --output-file Hotspot/Hotspot-GABP-GM12878-IDR2 --peak-list Hotspot/Hotspot-GABP-GM12878-Rep0.relaxed.narrowPeak.top300K.gz --rank signal.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 Hotspot/Hotspot-GABP-HELAS3-Rep1.relaxed.narrowPeak.top300K.gz Hotspot/Hotspot-GABP-HELAS3-Rep2.relaxed.narrowPeak.top300K.gz --input-file-type narrowPeak --output-file Hotspot/Hotspot-GABP-HELAS3-IDR2 --peak-list Hotspot/Hotspot-GABP-HELAS3-Rep0.relaxed.narrowPeak.top300K.gz --rank signal.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 Hotspot/Hotspot-P300-K562-Rep1.relaxed.narrowPeak.top300K.gz Hotspot/Hotspot-P300-K562-Rep2.relaxed.narrowPeak.top300K.gz --input-file-type narrowPeak --output-file Hotspot/Hotspot-P300-K562-IDR2 --peak-list Hotspot/Hotspot-P300-K562-Rep0.relaxed.narrowPeak.top300K.gz --rank signal.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 Hotspot/Hotspot-POL2-H1ESC-Rep1.relaxed.narrowPeak.top300K.gz Hotspot/Hotspot-POL2-H1ESC-Rep2.relaxed.narrowPeak.top300K.gz --input-file-type narrowPeak --output-file Hotspot/Hotspot-POL2-H1ESC-IDR2 --peak-list Hotspot/Hotspot-POL2-H1ESC-Rep0.relaxed.narrowPeak.top300K.gz --rank signal.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 Hotspot/Hotspot-POL2-H1NEURON-Rep1.relaxed.narrowPeak.top300K.gz Hotspot/Hotspot-POL2-H1NEURON-Rep2.relaxed.narrowPeak.top300K.gz --input-file-type narrowPeak --output-file Hotspot/Hotspot-POL2-H1NEURON-IDR2 --peak-list Hotspot/Hotspot-POL2-H1NEURON-Rep0.relaxed.narrowPeak.top300K.gz --rank signal.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 Hotspot/Hotspot-ZNF274-K562-Rep1.relaxed.narrowPeak.top300K.gz Hotspot/Hotspot-ZNF274-K562-Rep2.relaxed.narrowPeak.top300K.gz --input-file-type narrowPeak --output-file Hotspot/Hotspot-ZNF274-K562-IDR2 --peak-list Hotspot/Hotspot-ZNF274-K562-Rep0.relaxed.narrowPeak.top300K.gz --rank signal.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 Hotspotv2/Hotspotv2-CTCF-GM12878-Rep1.relaxed.narrowPeak.top300K.gz Hotspotv2/Hotspotv2-CTCF-GM12878-Rep2.relaxed.narrowPeak.top300K.gz --input-file-type narrowPeak --output-file Hotspotv2/Hotspotv2-CTCF-GM12878-IDR2 --peak-list Hotspotv2/Hotspotv2-CTCF-GM12878-Rep0.relaxed.narrowPeak.top300K.gz --rank signal.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 Hotspotv2/Hotspotv2-GABP-GM12878-Rep1.relaxed.narrowPeak.top300K.gz Hotspotv2/Hotspotv2-GABP-GM12878-Rep2.relaxed.narrowPeak.top300K.gz --input-file-type narrowPeak --output-file Hotspotv2/Hotspotv2-GABP-GM12878-IDR2 --peak-list Hotspotv2/Hotspotv2-GABP-GM12878-Rep0.relaxed.narrowPeak.top300K.gz --rank signal.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 Hotspotv2/Hotspotv2-GABP-HELAS3-Rep1.relaxed.narrowPeak.top300K.gz Hotspotv2/Hotspotv2-GABP-HELAS3-Rep2.relaxed.narrowPeak.top300K.gz --input-file-type narrowPeak --output-file Hotspotv2/Hotspotv2-GABP-HELAS3-IDR2 --peak-list Hotspotv2/Hotspotv2-GABP-HELAS3-Rep0.relaxed.narrowPeak.top300K.gz --rank signal.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 Hotspotv2/Hotspotv2-P300-K562-Rep1.relaxed.narrowPeak.top300K.gz Hotspotv2/Hotspotv2-P300-K562-Rep2.relaxed.narrowPeak.top300K.gz --input-file-type narrowPeak --output-file Hotspotv2/Hotspotv2-P300-K562-IDR2 --peak-list Hotspotv2/Hotspotv2-P300-K562-Rep0.relaxed.narrowPeak.top300K.gz --rank signal.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 Hotspotv2/Hotspotv2-POL2-H1ESC-Rep1.relaxed.narrowPeak.top300K.gz Hotspotv2/Hotspotv2-POL2-H1ESC-Rep2.relaxed.narrowPeak.top300K.gz --input-file-type narrowPeak --output-file Hotspotv2/Hotspotv2-POL2-H1ESC-IDR2 --peak-list Hotspotv2/Hotspotv2-POL2-H1ESC-Rep0.relaxed.narrowPeak.top300K.gz --rank signal.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 Hotspotv2/Hotspotv2-POL2-H1NEURON-Rep1.relaxed.narrowPeak.top300K.gz Hotspotv2/Hotspotv2-POL2-H1NEURON-Rep2.relaxed.narrowPeak.top300K.gz --input-file-type narrowPeak --output-file Hotspotv2/Hotspotv2-POL2-H1NEURON-IDR2 --peak-list Hotspotv2/Hotspotv2-POL2-H1NEURON-Rep0.relaxed.narrowPeak.top300K.gz --rank signal.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 Hotspotv2/Hotspotv2-ZNF274-K562-Rep1.relaxed.narrowPeak.top300K.gz Hotspotv2/Hotspotv2-ZNF274-K562-Rep2.relaxed.narrowPeak.top300K.gz --input-file-type narrowPeak --output-file Hotspotv2/Hotspotv2-ZNF274-K562-IDR2 --peak-list Hotspotv2/Hotspotv2-ZNF274-K562-Rep0.relaxed.narrowPeak.top300K.gz --rank signal.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 MACS2/MACS2-CTCF-GM12878-Rep1.relaxed.narrowPeak.top300K.gz MACS2/MACS2-CTCF-GM12878-Rep2.relaxed.narrowPeak.top300K.gz --input-file-type narrowPeak --output-file MACS2/MACS2-CTCF-GM12878-IDR2 --peak-list MACS2/MACS2-CTCF-GM12878-Rep0.relaxed.narrowPeak.top300K.gz --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 MACS2/MACS2-GABP-GM12878-Rep1.relaxed.narrowPeak.top300K.gz MACS2/MACS2-GABP-GM12878-Rep2.relaxed.narrowPeak.top300K.gz --input-file-type narrowPeak --output-file MACS2/MACS2-GABP-GM12878-IDR2 --peak-list MACS2/MACS2-GABP-GM12878-Rep0.relaxed.narrowPeak.top300K.gz --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 MACS2/MACS2-GABP-HelaS3-Rep1.relaxed.narrowPeak.top300K.gz MACS2/MACS2-GABP-HelaS3-Rep2.relaxed.narrowPeak.top300K.gz --input-file-type narrowPeak --output-file MACS2/MACS2-GABP-HelaS3-IDR2 --peak-list MACS2/MACS2-GABP-HelaS3-Rep0.relaxed.narrowPeak.top300K.gz --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 MACS2/MACS2-P300-K562-Rep1.relaxed.narrowPeak.top300K.gz MACS2/MACS2-P300-K562-Rep2.relaxed.narrowPeak.top300K.gz --input-file-type narrowPeak --output-file MACS2/MACS2-P300-K562-IDR2 --peak-list MACS2/MACS2-P300-K562-Rep0.relaxed.narrowPeak.top300K.gz --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 MACS2/MACS2-POL2-H1hesc-Rep1.relaxed.narrowPeak.top300K.gz MACS2/MACS2-POL2-H1hesc-Rep2.relaxed.narrowPeak.top300K.gz --input-file-type narrowPeak --output-file MACS2/MACS2-POL2-H1hesc-IDR2 --peak-list MACS2/MACS2-POL2-H1hesc-Rep0.relaxed.narrowPeak.top300K.gz --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 MACS2/MACS2-POL2-H1neuron-Rep1.relaxed.narrowPeak.top300K.gz MACS2/MACS2-POL2-H1neuron-Rep2.relaxed.narrowPeak.top300K.gz --input-file-type narrowPeak --output-file MACS2/MACS2-POL2-H1neuron-IDR2 --peak-list MACS2/MACS2-POL2-H1neuron-Rep0.relaxed.narrowPeak.top300K.gz --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 MACS2/MACS2-ZNF274-K562-Rep1.relaxed.narrowPeak.top300K.gz MACS2/MACS2-ZNF274-K562-Rep2.relaxed.narrowPeak.top300K.gz --input-file-type narrowPeak --output-file MACS2/MACS2-ZNF274-K562-IDR2 --peak-list MACS2/MACS2-ZNF274-K562-Rep0.relaxed.narrowPeak.top300K.gz --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 MOSAICS3/MOSAiCS3-CTCF-GM12878-Rep1.relaxed.narrowPeak.top300K.gz MOSAICS3/MOSAiCS3-CTCF-GM12878-Rep2.relaxed.narrowPeak.top300K.gz --input-file-type narrowPeak --output-file MOSAICS3/MOSAiCS3-CTCF-GM12878-IDR2 --peak-list MOSAICS3/MOSAiCS3-CTCF-GM12878-Rep0.relaxed.narrowPeak.top300K.gz --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 MOSAICS3/MOSAiCS3-GABP-GM12878-Rep1.relaxed.narrowPeak.top300K.gz MOSAICS3/MOSAiCS3-GABP-GM12878-Rep2.relaxed.narrowPeak.top300K.gz --input-file-type narrowPeak --output-file MOSAICS3/MOSAiCS3-GABP-GM12878-IDR2 --peak-list MOSAICS3/MOSAiCS3-GABP-GM12878-Rep0.relaxed.narrowPeak.top300K.gz --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 MOSAICS3/MOSAiCS3-GABP-HELAS3-Rep1.relaxed.narrowPeak.top300K.gz MOSAICS3/MOSAiCS3-GABP-HELAS3-Rep2.relaxed.narrowPeak.top300K.gz --input-file-type narrowPeak --output-file MOSAICS3/MOSAiCS3-GABP-HELAS3-IDR2 --peak-list MOSAICS3/MOSAiCS3-GABP-HELAS3-Rep0.relaxed.narrowPeak.top300K.gz --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 MOSAICS3/MOSAiCS3-P300-K562-Rep1.relaxed.narrowPeak.top300K.gz MOSAICS3/MOSAiCS3-P300-K562-Rep2.relaxed.narrowPeak.top300K.gz --input-file-type narrowPeak --output-file MOSAICS3/MOSAiCS3-P300-K562-IDR2 --peak-list MOSAICS3/MOSAiCS3-P300-K562-Rep0.relaxed.narrowPeak.top300K.gz --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 MOSAICS3/MOSAiCS3-POL2-H1ESC-Rep1.relaxed.narrowPeak.top300K.gz MOSAICS3/MOSAiCS3-POL2-H1ESC-Rep2.relaxed.narrowPeak.top300K.gz --input-file-type narrowPeak --output-file MOSAICS3/MOSAiCS3-POL2-H1ESC-IDR2 --peak-list MOSAICS3/MOSAiCS3-POL2-H1ESC-Rep0.relaxed.narrowPeak.top300K.gz --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 MOSAICS3/MOSAiCS3-POL2-H1NEURON-Rep1.relaxed.narrowPeak.top300K.gz MOSAICS3/MOSAiCS3-POL2-H1NEURON-Rep2.relaxed.narrowPeak.top300K.gz --input-file-type narrowPeak --output-file MOSAICS3/MOSAiCS3-POL2-H1NEURON-IDR2 --peak-list MOSAICS3/MOSAiCS3-POL2-H1NEURON-Rep0.relaxed.narrowPeak.top300K.gz --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 MOSAICS3/MOSAiCS3-ZNF274-K562-Rep1.relaxed.narrowPeak.top300K.gz MOSAICS3/MOSAiCS3-ZNF274-K562-Rep2.relaxed.narrowPeak.top300K.gz --input-file-type narrowPeak --output-file MOSAICS3/MOSAiCS3-ZNF274-K562-IDR2 --peak-list MOSAICS3/MOSAiCS3-ZNF274-K562-Rep0.relaxed.narrowPeak.top300K.gz --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 MOSAICS/MOSAiCS-CTCF-GM12878-Rep1.relaxed.narrowPeak.top300K.gz MOSAICS/MOSAiCS-CTCF-GM12878-Rep2.relaxed.narrowPeak.top300K.gz --input-file-type narrowPeak --output-file MOSAICS/MOSAiCS-CTCF-GM12878-IDR2 --peak-list MOSAICS/MOSAiCS-CTCF-GM12878-Rep0.relaxed.narrowPeak.top300K.gz --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 MOSAICS/MOSAiCS-GABP-GM12878-Rep1.relaxed.narrowPeak.top300K.gz MOSAICS/MOSAiCS-GABP-GM12878-Rep2.relaxed.narrowPeak.top300K.gz --input-file-type narrowPeak --output-file MOSAICS/MOSAiCS-GABP-GM12878-IDR2 --peak-list MOSAICS/MOSAiCS-GABP-GM12878-Rep0.relaxed.narrowPeak.top300K.gz --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 MOSAICS/MOSAiCS-GABP-HELAS3-Rep1.relaxed.narrowPeak.top300K.gz MOSAICS/MOSAiCS-GABP-HELAS3-Rep2.relaxed.narrowPeak.top300K.gz --input-file-type narrowPeak --output-file MOSAICS/MOSAiCS-GABP-HELAS3-IDR2 --peak-list MOSAICS/MOSAiCS-GABP-HELAS3-Rep0.relaxed.narrowPeak.top300K.gz --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 MOSAICS/MOSAiCS-P300-K562-Rep1.relaxed.narrowPeak.top300K.gz MOSAICS/MOSAiCS-P300-K562-Rep2.relaxed.narrowPeak.top300K.gz --input-file-type narrowPeak --output-file MOSAICS/MOSAiCS-P300-K562-IDR2 --peak-list MOSAICS/MOSAiCS-P300-K562-Rep0.relaxed.narrowPeak.top300K.gz --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 MOSAICS/MOSAiCS-POL2-H1ESC-Rep1.relaxed.narrowPeak.top300K.gz MOSAICS/MOSAiCS-POL2-H1ESC-Rep2.relaxed.narrowPeak.top300K.gz --input-file-type narrowPeak --output-file MOSAICS/MOSAiCS-POL2-H1ESC-IDR2 --peak-list MOSAICS/MOSAiCS-POL2-H1ESC-Rep0.relaxed.narrowPeak.top300K.gz --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 MOSAICS/MOSAiCS-POL2-H1NEURON-Rep1.relaxed.narrowPeak.top300K.gz MOSAICS/MOSAiCS-POL2-H1NEURON-Rep2.relaxed.narrowPeak.top300K.gz --input-file-type narrowPeak --output-file MOSAICS/MOSAiCS-POL2-H1NEURON-IDR2 --peak-list MOSAICS/MOSAiCS-POL2-H1NEURON-Rep0.relaxed.narrowPeak.top300K.gz --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 MOSAICS/MOSAiCS-ZNF274-K562-Rep1.relaxed.narrowPeak.top300K.gz MOSAICS/MOSAiCS-ZNF274-K562-Rep2.relaxed.narrowPeak.top300K.gz --input-file-type narrowPeak --output-file MOSAICS/MOSAiCS-ZNF274-K562-IDR2 --peak-list MOSAICS/MOSAiCS-ZNF274-K562-Rep0.relaxed.narrowPeak.top300K.gz --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 PeakSeq/PeakSeq-CTCF-GM12878-Rep1.relaxed.narrowPeak.top300K.gz PeakSeq/PeakSeq-CTCF-GM12878-Rep2.relaxed.narrowPeak.top300K.gz --input-file-type narrowPeak --output-file PeakSeq/PeakSeq-CTCF-GM12878-IDR2 --peak-list PeakSeq/PeakSeq-CTCF-GM12878-Rep0.relaxed.narrowPeak.top300K.gz --rank q.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 PeakSeq/PeakSeq-GABP-GM12878-Rep1.relaxed.narrowPeak.top300K.gz PeakSeq/PeakSeq-GABP-GM12878-Rep2.relaxed.narrowPeak.top300K.gz --input-file-type narrowPeak --output-file PeakSeq/PeakSeq-GABP-GM12878-IDR2 --peak-list PeakSeq/PeakSeq-GABP-GM12878-Rep0.relaxed.narrowPeak.top300K.gz --rank q.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 PeakSeq/PeakSeq-GABP-HELAS3-Rep1.relaxed.narrowPeak.top300K.gz PeakSeq/PeakSeq-GABP-HELAS3-Rep2.relaxed.narrowPeak.top300K.gz --input-file-type narrowPeak --output-file PeakSeq/PeakSeq-GABP-HELAS3-IDR2 --peak-list PeakSeq/PeakSeq-GABP-HELAS3-Rep0.relaxed.narrowPeak.top300K.gz --rank q.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 PeakSeq/PeakSeq-H1NEURON_NEW-Rep1.relaxed.narrowPeak.top300K.gz PeakSeq/PeakSeq-H1NEURON_NEW-Rep2.relaxed.narrowPeak.top300K.gz --input-file-type narrowPeak --output-file PeakSeq/PeakSeq-H1NEURON_NEW-IDR2 --peak-list PeakSeq/PeakSeq-H1NEURON_NEW-Rep0.relaxed.narrowPeak.top300K.gz --rank q.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 PeakSeq/PeakSeq-P300-K562-Rep1.relaxed.narrowPeak.top300K.gz PeakSeq/PeakSeq-P300-K562-Rep2.relaxed.narrowPeak.top300K.gz --input-file-type narrowPeak --output-file PeakSeq/PeakSeq-P300-K562-IDR2 --peak-list PeakSeq/PeakSeq-P300-K562-Rep0.relaxed.narrowPeak.top300K.gz --rank q.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 PeakSeq/PeakSeq-POL2-H1ESC-Rep1.relaxed.narrowPeak.top300K.gz PeakSeq/PeakSeq-POL2-H1ESC-Rep2.relaxed.narrowPeak.top300K.gz --input-file-type narrowPeak --output-file PeakSeq/PeakSeq-POL2-H1ESC-IDR2 --peak-list PeakSeq/PeakSeq-POL2-H1ESC-Rep0.relaxed.narrowPeak.top300K.gz --rank q.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 PeakSeq/PeakSeq-ZNF274-K562-Rep1.relaxed.narrowPeak.top300K.gz PeakSeq/PeakSeq-ZNF274-K562-Rep2.relaxed.narrowPeak.top300K.gz --input-file-type narrowPeak --output-file PeakSeq/PeakSeq-ZNF274-K562-IDR2 --peak-list PeakSeq/PeakSeq-ZNF274-K562-Rep0.relaxed.narrowPeak.top300K.gz --rank q.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 Scripture/Scripture-CTCF-GM12878-Rep1.relaxed.narrowPeak.top300K.gz Scripture/Scripture-CTCF-GM12878-Rep2.relaxed.narrowPeak.top300K.gz --input-file-type narrowPeak --output-file Scripture/Scripture-CTCF-GM12878-IDR2 --peak-list Scripture/Scripture-CTCF-GM12878-Rep0.relaxed.narrowPeak.top300K.gz --rank signal.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 Scripture/Scripture-GABP-GM12878-Rep1.relaxed.narrowPeak.top300K.gz Scripture/Scripture-GABP-GM12878-Rep2.relaxed.narrowPeak.top300K.gz --input-file-type narrowPeak --output-file Scripture/Scripture-GABP-GM12878-IDR2 --peak-list Scripture/Scripture-GABP-GM12878-Rep0.relaxed.narrowPeak.top300K.gz --rank signal.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 Scripture/Scripture-GABP-HELAS3-Rep1.relaxed.narrowPeak.top300K.gz Scripture/Scripture-GABP-HELAS3-Rep2.relaxed.narrowPeak.top300K.gz --input-file-type narrowPeak --output-file Scripture/Scripture-GABP-HELAS3-IDR2 --peak-list Scripture/Scripture-GABP-HELAS3-Rep0.relaxed.narrowPeak.top300K.gz --rank signal.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 Scripture/Scripture-P300-K562-Rep1.relaxed.narrowPeak.top300K.gz Scripture/Scripture-P300-K562-Rep2.relaxed.narrowPeak.top300K.gz --input-file-type narrowPeak --output-file Scripture/Scripture-P300-K562-IDR2 --peak-list Scripture/Scripture-P300-K562-Rep0.relaxed.narrowPeak.top300K.gz --rank signal.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 Scripture/Scripture-POL2-H1ESC-Rep1.relaxed.narrowPeak.top300K.gz Scripture/Scripture-POL2-H1ESC-Rep2.relaxed.narrowPeak.top300K.gz --input-file-type narrowPeak --output-file Scripture/Scripture-POL2-H1ESC-IDR2 --peak-list Scripture/Scripture-POL2-H1ESC-Rep0.relaxed.narrowPeak.top300K.gz --rank signal.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 Scripture/Scripture-POL2-H1NEURON-Rep1.relaxed.narrowPeak.top300K.gz Scripture/Scripture-POL2-H1NEURON-Rep2.relaxed.narrowPeak.top300K.gz --input-file-type narrowPeak --output-file Scripture/Scripture-POL2-H1NEURON-IDR2 --peak-list Scripture/Scripture-POL2-H1NEURON-Rep0.relaxed.narrowPeak.top300K.gz --rank signal.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 Scripture/Scripture-ZNF274-K562-Rep1.relaxed.narrowPeak.top300K.gz Scripture/Scripture-ZNF274-K562-Rep2.relaxed.narrowPeak.top300K.gz --input-file-type narrowPeak --output-file Scripture/Scripture-ZNF274-K562-IDR2 --peak-list Scripture/Scripture-ZNF274-K562-Rep0.relaxed.narrowPeak.top300K.gz --rank signal.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 SPP/SPP-CTCF-GM12878-Rep1.relaxed.narrowPeak.top300K.gz SPP/SPP-CTCF-GM12878-Rep2.relaxed.narrowPeak.top300K.gz --input-file-type narrowPeak --output-file SPP/SPP-CTCF-GM12878-IDR2 --peak-list SPP/SPP-CTCF-GM12878-Rep0.relaxed.narrowPeak.top300K.gz --rank signal.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 SPP/SPP-GABP-GM12878-Rep1.relaxed.narrowPeak.top300K.gz SPP/SPP-GABP-GM12878-Rep2.relaxed.narrowPeak.top300K.gz --input-file-type narrowPeak --output-file SPP/SPP-GABP-GM12878-IDR2 --peak-list SPP/SPP-GABP-GM12878-Rep0.relaxed.narrowPeak.top300K.gz --rank signal.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 SPP/SPP-GABP-HELAS3-Rep1.relaxed.narrowPeak.top300K.gz SPP/SPP-GABP-HELAS3-Rep2.relaxed.narrowPeak.top300K.gz --input-file-type narrowPeak --output-file SPP/SPP-GABP-HELAS3-IDR2 --peak-list SPP/SPP-GABP-HELAS3-Rep0.relaxed.narrowPeak.top300K.gz --rank signal.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 SPP/SPP-P300-K562-Rep1.relaxed.narrowPeak.top300K.gz SPP/SPP-P300-K562-Rep2.relaxed.narrowPeak.top300K.gz --input-file-type narrowPeak --output-file SPP/SPP-P300-K562-IDR2 --peak-list SPP/SPP-P300-K562-Rep0.relaxed.narrowPeak.top300K.gz --rank signal.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 SPP/SPP-POL2-H1ESC-Rep1.relaxed.narrowPeak.top300K.gz SPP/SPP-POL2-H1ESC-Rep2.relaxed.narrowPeak.top300K.gz --input-file-type narrowPeak --output-file SPP/SPP-POL2-H1ESC-IDR2 --peak-list SPP/SPP-POL2-H1ESC-Rep0.relaxed.narrowPeak.top300K.gz --rank signal.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 SPP/SPP-POL2-H1NEURON-Rep1.relaxed.narrowPeak.top300K.gz SPP/SPP-POL2-H1NEURON-Rep2.relaxed.narrowPeak.top300K.gz --input-file-type narrowPeak --output-file SPP/SPP-POL2-H1NEURON-IDR2 --peak-list SPP/SPP-POL2-H1NEURON-Rep0.relaxed.narrowPeak.top300K.gz --rank signal.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 SPP/SPP-ZNF274-K562-Rep1.relaxed.narrowPeak.top300K.gz SPP/SPP-ZNF274-K562-Rep2.relaxed.narrowPeak.top300K.gz --input-file-type narrowPeak --output-file SPP/SPP-ZNF274-K562-IDR2 --peak-list SPP/SPP-ZNF274-K562-Rep0.relaxed.narrowPeak.top300K.gz --rank signal.value --soft-idr-threshold 0.05 --plot --use-best-multisummit-IDR