module load python/3.6.1; /oak/stanford/groups/akundaje/marinovg/programs/idr-2.0.4/bin/idr --samples Oct4-ChIPseq-shCtrl-GSM1562331.36mers.unique.dedup.pseudoRep1.MACS-2.1.0.p1e-1_peaks.narrowPeak.sorted.gz Oct4-ChIPseq-shCtrl-GSM1562331.36mers.unique.dedup.pseudoRep2.MACS-2.1.0.p1e-1_peaks.narrowPeak.sorted.gz --input-file-type narrowPeak --output-file Oct4-ChIPseq-shCtrl-GSM1562331.36mers.unique.dedup.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 Oct4-DamID.merged.pseudoRep1.MACS-2.1.0.p1e-1_peaks.narrowPeak.sorted.gz Oct4-DamID.merged.pseudoRep2.MACS-2.1.0.p1e-1_peaks.narrowPeak.sorted.gz --input-file-type narrowPeak --output-file Oct4-DamID.merged.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 Oct4-DamID-r1-GSM1562327.36mers.unique.MACS-2.1.0.p1e-1_peaks.narrowPeak.sorted.gz Oct4-DamID-r2-GSM1562328.36mers.unique.MACS-2.1.0.p1e-1_peaks.narrowPeak.sorted.gz --input-file-type narrowPeak --output-file Oct4-DamID.indReps.IDR --rank p.value --soft-idr-threshold 0.05 --plot --use-best-multisummit-IDR