module load python/3.6.1; /oak/stanford/groups/akundaje/marinovg/programs/idr-2.0.4/bin/idr --samples BCL6_FA_ChIP-seq-GSM2754207-vs-FA_IgG_control-GSM2754209.dedup.pseudoRep1.MACS-2.1.0.p1e-1_peaks.narrowPeak.sorted.gz BCL6_FA_ChIP-seq-GSM2754207-vs-FA_IgG_control-GSM2754209.dedup.pseudoRep2.MACS-2.1.0.p1e-1_peaks.narrowPeak.sorted.gz --input-file-type narrowPeak --output-file BCL6_FA_ChIP-seq-GSM2754207-vs-FA_IgG_control-GSM2754209.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 BCL6_FA_ChIP-seq-GSM2754207-vs-FA_input_DNA-GSM2754208.dedup.pseudoRep1.MACS-2.1.0.p1e-1_peaks.narrowPeak.sorted.gz BCL6_FA_ChIP-seq-GSM2754207-vs-FA_input_DNA-GSM2754208.dedup.pseudoRep2.MACS-2.1.0.p1e-1_peaks.narrowPeak.sorted.gz --input-file-type narrowPeak --output-file BCL6_FA_ChIP-seq-GSM2754207-vs-FA_input_DNA-GSM2754208.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 BCL6_UV-ChIP-seq_merged-vs-minusUV_control_ChIP-GSM2754206.dedup.pseudoRep1.MACS-2.1.0.p1e-1_peaks.narrowPeak.sorted.gz BCL6_UV-ChIP-seq_merged-vs-minusUV_control_ChIP-GSM2754206.dedup.pseudoRep2.MACS-2.1.0.p1e-1_peaks.narrowPeak.sorted.gz --input-file-type narrowPeak --output-file BCL6_UV-ChIP-seq_merged-vs-minusUV_control_ChIP-GSM2754206.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 BCL6_UV-ChIP-seq_merged-vs-UV_IgG_control-GSM2754205.dedup.pseudoRep1.MACS-2.1.0.p1e-1_peaks.narrowPeak.sorted.gz BCL6_UV-ChIP-seq_merged-vs-UV_IgG_control-GSM2754205.dedup.pseudoRep2.MACS-2.1.0.p1e-1_peaks.narrowPeak.sorted.gz --input-file-type narrowPeak --output-file BCL6_UV-ChIP-seq_merged-vs-UV_IgG_control-GSM2754205.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 BCL6_UV-ChIP-seq_merged-vs-UV_input_DNA-GSM2754204.dedup.pseudoRep1.MACS-2.1.0.p1e-1_peaks.narrowPeak.sorted.gz BCL6_UV-ChIP-seq_merged-vs-UV_input_DNA-GSM2754204.dedup.pseudoRep2.MACS-2.1.0.p1e-1_peaks.narrowPeak.sorted.gz --input-file-type narrowPeak --output-file BCL6_UV-ChIP-seq_merged-vs-UV_input_DNA-GSM2754204.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 BCL6_UV-ChIP-seq_repl1-GSM2754202-vs-minusUV_control_ChIP-GSM2754206.dedup.MACS-2.1.0.p1e-1_peaks.narrowPeak.sorted.gz BCL6_UV-ChIP-seq_repl2-GSM2754203-vs-minusUV_control_ChIP-GSM2754206.dedup.MACS-2.1.0.p1e-1_peaks.narrowPeak.sorted.gz --input-file-type narrowPeak --output-file BCL6_UV-ChIP-seq-vs-minusUV_control_ChIP-GSM2754206.dedup.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 BCL6_UV-ChIP-seq_repl1-GSM2754202-vs-UV_IgG_control-GSM2754205.dedup.MACS-2.1.0.p1e-1_peaks.narrowPeak.sorted.gz BCL6_UV-ChIP-seq_repl2-GSM2754203-vs-UV_IgG_control-GSM2754205.dedup.MACS-2.1.0.p1e-1_peaks.narrowPeak.sorted.gz --input-file-type narrowPeak --output-file BCL6_UV-ChIP-seq-vs-UV_IgG_control-GSM2754205.dedup.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 BCL6_UV-ChIP-seq_repl1-GSM2754202-vs-UV_input_DNA-GSM2754204.dedup.MACS-2.1.0.p1e-1_peaks.narrowPeak.sorted.gz BCL6_UV-ChIP-seq_repl2-GSM2754203-vs-UV_input_DNA-GSM2754204.dedup.MACS-2.1.0.p1e-1_peaks.narrowPeak.sorted.gz --input-file-type narrowPeak --output-file BCL6_UV-ChIP-seq-vs-UV_input_DNA-GSM2754204.dedup.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 GSE29282-OCI-LY1_BCL6_D-8_CHIP-GSM763404.36mers.unique.dedup.pseudoRep1.MACS-2.1.0.p1e-1_peaks.narrowPeak.sorted.gz GSE29282-OCI-LY1_BCL6_D-8_CHIP-GSM763404.36mers.unique.dedup.pseudoRep2.dedup.pseudoRep2.MACS-2.1.0.p1e-1_peaks.narrowPeak.sorted.gz --input-file-type narrowPeak --output-file GSE29282-OCI-LY1_BCL6_D-8_CHIP-GSM763404.36mers.unique.dedup.pseudoReps.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 GSE29282-OCI-LY1_BCL6_N-3_rep2_CHIP-GSM763402.36mers.unique.dedup.pseudoRep1.MACS-2.1.0.p1e-1_peaks.narrowPeak.sorted.gz GSE29282-OCI-LY1_BCL6_N-3_rep2_CHIP-GSM763402.36mers.unique.dedup.pseudoRep2.dedup.pseudoRep2.MACS-2.1.0.p1e-1_peaks.narrowPeak.sorted.gz --input-file-type narrowPeak --output-file GSE29282-OCI-LY1_BCL6_N-3_rep2_CHIP-GSM763402.36mers.unique.dedup.pseudoReps.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 GSE46663-LY1_BCL6_DMSO-GSM1133657.36mers.unique.dedup.pseudoRep1.MACS-2.1.0.p1e-1_peaks.narrowPeak.sorted.gz GSE46663-LY1_BCL6_DMSO-GSM1133657.36mers.unique.dedup.pseudoRep2.dedup.pseudoRep2.MACS-2.1.0.p1e-1_peaks.narrowPeak.sorted.gz --input-file-type narrowPeak --output-file GSE46663-LY1_BCL6_DMSO-GSM1133657.36mers.unique.dedup.pseudoReps.dedup.pseudoReps.IDR  --rank p.value --soft-idr-threshold 0.05 --plot --use-best-multisummit-IDR