module load python/3.6.1; /oak/stanford/groups/akundaje/marinovg/programs/idr-2.0.4/bin/idr --samples AWRI1631-ATAC.2x50mers.sacCer3_updated.noInDels.bowtie.unique.dedup.merged.sorted.pseudoRep1.MACS-2.1.0.p1e-1_peaks.narrowPeak AWRI1631-ATAC.2x50mers.sacCer3_updated.noInDels.bowtie.unique.dedup.merged.sorted.pseudoRep2.MACS-2.1.0.p1e-1_peaks.narrowPeak --input-file-type narrowPeak --rank p.value --soft-idr-threshold 0.05 --plot --use-best-multisummit-IDR --peak-list AWRI1631-ATAC.2x50mers.sacCer3_updated.noInDels.bowtie.unique.dedup.merged.sorted.MACS-2.1.0.p1e-1_peaks.narrowPeak --output-file AWRI1631-ATAC.2x50mers.sacCer3_updated.noInDels.bowtie.unique.dedup.pooled.MACS2.IDR
module load python/3.6.1; /oak/stanford/groups/akundaje/marinovg/programs/idr-2.0.4/bin/idr --samples BY4741-ATAC.2x50mers.sacCer3_updated.noInDels.bowtie.unique.dedup.merged.sorted.pseudoRep1.MACS-2.1.0.p1e-1_peaks.narrowPeak BY4741-ATAC.2x50mers.sacCer3_updated.noInDels.bowtie.unique.dedup.merged.sorted.pseudoRep2.MACS-2.1.0.p1e-1_peaks.narrowPeak --input-file-type narrowPeak --rank p.value --soft-idr-threshold 0.05 --plot --use-best-multisummit-IDR --peak-list BY4741-ATAC.2x50mers.sacCer3_updated.noInDels.bowtie.unique.dedup.merged.sorted.MACS-2.1.0.p1e-1_peaks.narrowPeak --output-file BY4741-ATAC.2x50mers.sacCer3_updated.noInDels.bowtie.unique.dedup.pooled.MACS2.IDR
module load python/3.6.1; /oak/stanford/groups/akundaje/marinovg/programs/idr-2.0.4/bin/idr --samples BY4742-ATAC.2x50mers.sacCer3_updated.noInDels.bowtie.unique.dedup.merged.sorted.pseudoRep1.MACS-2.1.0.p1e-1_peaks.narrowPeak BY4742-ATAC.2x50mers.sacCer3_updated.noInDels.bowtie.unique.dedup.merged.sorted.pseudoRep2.MACS-2.1.0.p1e-1_peaks.narrowPeak --input-file-type narrowPeak --rank p.value --soft-idr-threshold 0.05 --plot --use-best-multisummit-IDR --peak-list BY4742-ATAC.2x50mers.sacCer3_updated.noInDels.bowtie.unique.dedup.merged.sorted.MACS-2.1.0.p1e-1_peaks.narrowPeak --output-file BY4742-ATAC.2x50mers.sacCer3_updated.noInDels.bowtie.unique.dedup.pooled.MACS2.IDR
module load python/3.6.1; /oak/stanford/groups/akundaje/marinovg/programs/idr-2.0.4/bin/idr --samples RM11_1a-ATAC.2x50mers.sacCer3_updated.noInDels.bowtie.unique.dedup.merged.sorted.pseudoRep1.MACS-2.1.0.p1e-1_peaks.narrowPeak RM11_1a-ATAC.2x50mers.sacCer3_updated.noInDels.bowtie.unique.dedup.merged.sorted.pseudoRep2.MACS-2.1.0.p1e-1_peaks.narrowPeak --input-file-type narrowPeak --rank p.value --soft-idr-threshold 0.05 --plot --use-best-multisummit-IDR --peak-list RM11_1a-ATAC.2x50mers.sacCer3_updated.noInDels.bowtie.unique.dedup.merged.sorted.MACS-2.1.0.p1e-1_peaks.narrowPeak --output-file RM11_1a-ATAC.2x50mers.sacCer3_updated.noInDels.bowtie.unique.dedup.pooled.MACS2.IDR
module load python/3.6.1; /oak/stanford/groups/akundaje/marinovg/programs/idr-2.0.4/bin/idr --samples YJM789-ATAC.2x50mers.sacCer3_updated.noInDels.bowtie.unique.dedup.merged.sorted.pseudoRep1.MACS-2.1.0.p1e-1_peaks.narrowPeak YJM789-ATAC.2x50mers.sacCer3_updated.noInDels.bowtie.unique.dedup.merged.sorted.pseudoRep2.MACS-2.1.0.p1e-1_peaks.narrowPeak --input-file-type narrowPeak --rank p.value --soft-idr-threshold 0.05 --plot --use-best-multisummit-IDR --peak-list YJM789-ATAC.2x50mers.sacCer3_updated.noInDels.bowtie.unique.dedup.merged.sorted.MACS-2.1.0.p1e-1_peaks.narrowPeak --output-file YJM789-ATAC.2x50mers.sacCer3_updated.noInDels.bowtie.unique.dedup.pooled.MACS2.IDR
module load python/3.6.1; /oak/stanford/groups/akundaje/marinovg/programs/idr-2.0.4/bin/idr --samples AWRI1631-ATAC-Rep1/AWRI1631-ATAC-Rep1.2x50mers.sacCer3_updated.noInDels.bowtie.unique.dedup.pseudoRep1.MACS-2.1.0.p1e-1_peaks.narrowPeak AWRI1631-ATAC-Rep1/AWRI1631-ATAC-Rep1.2x50mers.sacCer3_updated.noInDels.bowtie.unique.dedup.pseudoRep2.MACS-2.1.0.p1e-1_peaks.narrowPeak --input-file-type narrowPeak --rank p.value --soft-idr-threshold 0.05 --plot --use-best-multisummit-IDR --peak-list AWRI1631-ATAC-Rep1/AWRI1631-ATAC-Rep1.2x50mers.sacCer3_updated.noInDels.bowtie.unique.dedup.MACS-2.1.0.p1e-1_peaks.narrowPeak --output-file AWRI1631-ATAC-Rep1/AWRI1631-ATAC-Rep1.2x50mers.sacCer3_updated.noInDels.bowtie.unique.dedup.ind_pseudo_rep.MACS2.IDR
module load python/3.6.1; /oak/stanford/groups/akundaje/marinovg/programs/idr-2.0.4/bin/idr --samples AWRI1631-ATAC-Rep2/AWRI1631-ATAC-Rep2.2x50mers.sacCer3_updated.noInDels.bowtie.unique.dedup.pseudoRep1.MACS-2.1.0.p1e-1_peaks.narrowPeak AWRI1631-ATAC-Rep2/AWRI1631-ATAC-Rep2.2x50mers.sacCer3_updated.noInDels.bowtie.unique.dedup.pseudoRep2.MACS-2.1.0.p1e-1_peaks.narrowPeak --input-file-type narrowPeak --rank p.value --soft-idr-threshold 0.05 --plot --use-best-multisummit-IDR --peak-list AWRI1631-ATAC-Rep2/AWRI1631-ATAC-Rep2.2x50mers.sacCer3_updated.noInDels.bowtie.unique.dedup.MACS-2.1.0.p1e-1_peaks.narrowPeak --output-file AWRI1631-ATAC-Rep2/AWRI1631-ATAC-Rep2.2x50mers.sacCer3_updated.noInDels.bowtie.unique.dedup.ind_pseudo_rep.MACS2.IDR
module load python/3.6.1; /oak/stanford/groups/akundaje/marinovg/programs/idr-2.0.4/bin/idr --samples BY4741-ATAC-Rep1/BY4741-ATAC-Rep1.2x50mers.sacCer3_updated.noInDels.bowtie.unique.dedup.pseudoRep1.MACS-2.1.0.p1e-1_peaks.narrowPeak BY4741-ATAC-Rep1/BY4741-ATAC-Rep1.2x50mers.sacCer3_updated.noInDels.bowtie.unique.dedup.pseudoRep2.MACS-2.1.0.p1e-1_peaks.narrowPeak --input-file-type narrowPeak --rank p.value --soft-idr-threshold 0.05 --plot --use-best-multisummit-IDR --peak-list BY4741-ATAC-Rep1/BY4741-ATAC-Rep1.2x50mers.sacCer3_updated.noInDels.bowtie.unique.dedup.MACS-2.1.0.p1e-1_peaks.narrowPeak --output-file BY4741-ATAC-Rep1/BY4741-ATAC-Rep1.2x50mers.sacCer3_updated.noInDels.bowtie.unique.dedup.ind_pseudo_rep.MACS2.IDR
module load python/3.6.1; /oak/stanford/groups/akundaje/marinovg/programs/idr-2.0.4/bin/idr --samples BY4741-ATAC-Rep2/BY4741-ATAC-Rep2.2x50mers.sacCer3_updated.noInDels.bowtie.unique.dedup.pseudoRep1.MACS-2.1.0.p1e-1_peaks.narrowPeak BY4741-ATAC-Rep2/BY4741-ATAC-Rep2.2x50mers.sacCer3_updated.noInDels.bowtie.unique.dedup.pseudoRep2.MACS-2.1.0.p1e-1_peaks.narrowPeak --input-file-type narrowPeak --rank p.value --soft-idr-threshold 0.05 --plot --use-best-multisummit-IDR --peak-list BY4741-ATAC-Rep2/BY4741-ATAC-Rep2.2x50mers.sacCer3_updated.noInDels.bowtie.unique.dedup.MACS-2.1.0.p1e-1_peaks.narrowPeak --output-file BY4741-ATAC-Rep2/BY4741-ATAC-Rep2.2x50mers.sacCer3_updated.noInDels.bowtie.unique.dedup.ind_pseudo_rep.MACS2.IDR
module load python/3.6.1; /oak/stanford/groups/akundaje/marinovg/programs/idr-2.0.4/bin/idr --samples BY4742-ATAC-Rep1/BY4742-ATAC-Rep1.2x50mers.sacCer3_updated.noInDels.bowtie.unique.dedup.pseudoRep1.MACS-2.1.0.p1e-1_peaks.narrowPeak BY4742-ATAC-Rep1/BY4742-ATAC-Rep1.2x50mers.sacCer3_updated.noInDels.bowtie.unique.dedup.pseudoRep2.MACS-2.1.0.p1e-1_peaks.narrowPeak --input-file-type narrowPeak --rank p.value --soft-idr-threshold 0.05 --plot --use-best-multisummit-IDR --peak-list BY4742-ATAC-Rep1/BY4742-ATAC-Rep1.2x50mers.sacCer3_updated.noInDels.bowtie.unique.dedup.MACS-2.1.0.p1e-1_peaks.narrowPeak --output-file BY4742-ATAC-Rep1/BY4742-ATAC-Rep1.2x50mers.sacCer3_updated.noInDels.bowtie.unique.dedup.ind_pseudo_rep.MACS2.IDR
module load python/3.6.1; /oak/stanford/groups/akundaje/marinovg/programs/idr-2.0.4/bin/idr --samples BY4742-ATAC-Rep2/BY4742-ATAC-Rep2.2x50mers.sacCer3_updated.noInDels.bowtie.unique.dedup.pseudoRep1.MACS-2.1.0.p1e-1_peaks.narrowPeak BY4742-ATAC-Rep2/BY4742-ATAC-Rep2.2x50mers.sacCer3_updated.noInDels.bowtie.unique.dedup.pseudoRep2.MACS-2.1.0.p1e-1_peaks.narrowPeak --input-file-type narrowPeak --rank p.value --soft-idr-threshold 0.05 --plot --use-best-multisummit-IDR --peak-list BY4742-ATAC-Rep2/BY4742-ATAC-Rep2.2x50mers.sacCer3_updated.noInDels.bowtie.unique.dedup.MACS-2.1.0.p1e-1_peaks.narrowPeak --output-file BY4742-ATAC-Rep2/BY4742-ATAC-Rep2.2x50mers.sacCer3_updated.noInDels.bowtie.unique.dedup.ind_pseudo_rep.MACS2.IDR
module load python/3.6.1; /oak/stanford/groups/akundaje/marinovg/programs/idr-2.0.4/bin/idr --samples RM11_1a-ATAC-Rep1/RM11_1a-ATAC-Rep1.2x50mers.sacCer3_updated.noInDels.bowtie.unique.dedup.pseudoRep1.MACS-2.1.0.p1e-1_peaks.narrowPeak RM11_1a-ATAC-Rep1/RM11_1a-ATAC-Rep1.2x50mers.sacCer3_updated.noInDels.bowtie.unique.dedup.pseudoRep2.MACS-2.1.0.p1e-1_peaks.narrowPeak --input-file-type narrowPeak --rank p.value --soft-idr-threshold 0.05 --plot --use-best-multisummit-IDR --peak-list RM11_1a-ATAC-Rep1/RM11_1a-ATAC-Rep1.2x50mers.sacCer3_updated.noInDels.bowtie.unique.dedup.MACS-2.1.0.p1e-1_peaks.narrowPeak --output-file RM11_1a-ATAC-Rep1/RM11_1a-ATAC-Rep1.2x50mers.sacCer3_updated.noInDels.bowtie.unique.dedup.ind_pseudo_rep.MACS2.IDR
module load python/3.6.1; /oak/stanford/groups/akundaje/marinovg/programs/idr-2.0.4/bin/idr --samples RM11_1a-ATAC-Rep2/RM11_1a-ATAC-Rep2.2x50mers.sacCer3_updated.noInDels.bowtie.unique.dedup.pseudoRep1.MACS-2.1.0.p1e-1_peaks.narrowPeak RM11_1a-ATAC-Rep2/RM11_1a-ATAC-Rep2.2x50mers.sacCer3_updated.noInDels.bowtie.unique.dedup.pseudoRep2.MACS-2.1.0.p1e-1_peaks.narrowPeak --input-file-type narrowPeak --rank p.value --soft-idr-threshold 0.05 --plot --use-best-multisummit-IDR --peak-list RM11_1a-ATAC-Rep2/RM11_1a-ATAC-Rep2.2x50mers.sacCer3_updated.noInDels.bowtie.unique.dedup.MACS-2.1.0.p1e-1_peaks.narrowPeak --output-file RM11_1a-ATAC-Rep2/RM11_1a-ATAC-Rep2.2x50mers.sacCer3_updated.noInDels.bowtie.unique.dedup.ind_pseudo_rep.MACS2.IDR
module load python/3.6.1; /oak/stanford/groups/akundaje/marinovg/programs/idr-2.0.4/bin/idr --samples YJM789-ATAC-Rep1/YJM789-ATAC-Rep1.2x50mers.sacCer3_updated.noInDels.bowtie.unique.dedup.pseudoRep1.MACS-2.1.0.p1e-1_peaks.narrowPeak YJM789-ATAC-Rep1/YJM789-ATAC-Rep1.2x50mers.sacCer3_updated.noInDels.bowtie.unique.dedup.pseudoRep2.MACS-2.1.0.p1e-1_peaks.narrowPeak --input-file-type narrowPeak --rank p.value --soft-idr-threshold 0.05 --plot --use-best-multisummit-IDR --peak-list YJM789-ATAC-Rep1/YJM789-ATAC-Rep1.2x50mers.sacCer3_updated.noInDels.bowtie.unique.dedup.MACS-2.1.0.p1e-1_peaks.narrowPeak --output-file YJM789-ATAC-Rep1/YJM789-ATAC-Rep1.2x50mers.sacCer3_updated.noInDels.bowtie.unique.dedup.ind_pseudo_rep.MACS2.IDR
module load python/3.6.1; /oak/stanford/groups/akundaje/marinovg/programs/idr-2.0.4/bin/idr --samples YJM789-ATAC-Rep2/YJM789-ATAC-Rep2.2x50mers.sacCer3_updated.noInDels.bowtie.unique.dedup.pseudoRep1.MACS-2.1.0.p1e-1_peaks.narrowPeak YJM789-ATAC-Rep2/YJM789-ATAC-Rep2.2x50mers.sacCer3_updated.noInDels.bowtie.unique.dedup.pseudoRep2.MACS-2.1.0.p1e-1_peaks.narrowPeak --input-file-type narrowPeak --rank p.value --soft-idr-threshold 0.05 --plot --use-best-multisummit-IDR --peak-list YJM789-ATAC-Rep2/YJM789-ATAC-Rep2.2x50mers.sacCer3_updated.noInDels.bowtie.unique.dedup.MACS-2.1.0.p1e-1_peaks.narrowPeak --output-file YJM789-ATAC-Rep2/YJM789-ATAC-Rep2.2x50mers.sacCer3_updated.noInDels.bowtie.unique.dedup.ind_pseudo_rep.MACS2.IDR
module load python/3.6.1; /oak/stanford/groups/akundaje/marinovg/programs/idr-2.0.4/bin/idr --samples AWRI1631-ATAC-Rep1/AWRI1631-ATAC-Rep1.2x50mers.sacCer3_updated.noInDels.bowtie.unique.dedup.MACS-2.1.0.p1e-1_peaks.narrowPeak AWRI1631-ATAC-Rep2/AWRI1631-ATAC-Rep2.2x50mers.sacCer3_updated.noInDels.bowtie.unique.dedup.MACS-2.1.0.p1e-1_peaks.narrowPeak --input-file-type narrowPeak --rank signal.value --soft-idr-threshold 0.05 --plot --use-best-multisummit-IDR --peak-list AWRI1631-ATAC.2x50mers.sacCer3_updated.noInDels.bowtie.unique.dedup.merged.sorted.MACS-2.1.0.p1e-1_peaks.narrowPeak --output-file AWRI1631-ATAC-Rep1-vs-AWRI1631-ATAC-Rep2.2x50mers.sacCer3_updated.noInDels.bowtie.unique.dedup.ind-reps.MACS2.IDR
module load python/3.6.1; /oak/stanford/groups/akundaje/marinovg/programs/idr-2.0.4/bin/idr --samples BY4741-ATAC-Rep1/BY4741-ATAC-Rep1.2x50mers.sacCer3_updated.noInDels.bowtie.unique.dedup.MACS-2.1.0.p1e-1_peaks.narrowPeak BY4741-ATAC-Rep2/BY4741-ATAC-Rep2.2x50mers.sacCer3_updated.noInDels.bowtie.unique.dedup.MACS-2.1.0.p1e-1_peaks.narrowPeak --input-file-type narrowPeak --rank signal.value --soft-idr-threshold 0.05 --plot --use-best-multisummit-IDR --peak-list BY4741-ATAC.2x50mers.sacCer3_updated.noInDels.bowtie.unique.dedup.merged.sorted.MACS-2.1.0.p1e-1_peaks.narrowPeak --output-file BY4741-ATAC-Rep1-vs-BY4741-ATAC-Rep2.2x50mers.sacCer3_updated.noInDels.bowtie.unique.dedup.ind-reps.MACS2.IDR
module load python/3.6.1; /oak/stanford/groups/akundaje/marinovg/programs/idr-2.0.4/bin/idr --samples BY4742-ATAC-Rep1/BY4742-ATAC-Rep1.2x50mers.sacCer3_updated.noInDels.bowtie.unique.dedup.MACS-2.1.0.p1e-1_peaks.narrowPeak BY4742-ATAC-Rep2/BY4742-ATAC-Rep2.2x50mers.sacCer3_updated.noInDels.bowtie.unique.dedup.MACS-2.1.0.p1e-1_peaks.narrowPeak --input-file-type narrowPeak --rank signal.value --soft-idr-threshold 0.05 --plot --use-best-multisummit-IDR --peak-list BY4742-ATAC.2x50mers.sacCer3_updated.noInDels.bowtie.unique.dedup.merged.sorted.MACS-2.1.0.p1e-1_peaks.narrowPeak --output-file BY4742-ATAC-Rep1-vs-BY4742-ATAC-Rep2.2x50mers.sacCer3_updated.noInDels.bowtie.unique.dedup.ind-reps.MACS2.IDR
module load python/3.6.1; /oak/stanford/groups/akundaje/marinovg/programs/idr-2.0.4/bin/idr --samples RM11_1a-ATAC-Rep1/RM11_1a-ATAC-Rep1.2x50mers.sacCer3_updated.noInDels.bowtie.unique.dedup.MACS-2.1.0.p1e-1_peaks.narrowPeak RM11_1a-ATAC-Rep2/RM11_1a-ATAC-Rep2.2x50mers.sacCer3_updated.noInDels.bowtie.unique.dedup.MACS-2.1.0.p1e-1_peaks.narrowPeak --input-file-type narrowPeak --rank signal.value --soft-idr-threshold 0.05 --plot --use-best-multisummit-IDR --peak-list RM11_1a-ATAC.2x50mers.sacCer3_updated.noInDels.bowtie.unique.dedup.merged.sorted.MACS-2.1.0.p1e-1_peaks.narrowPeak --output-file RM11_1a-ATAC-Rep1-vs-RM11_1a-ATAC-Rep2.2x50mers.sacCer3_updated.noInDels.bowtie.unique.dedup.ind-reps.MACS2.IDR
module load python/3.6.1; /oak/stanford/groups/akundaje/marinovg/programs/idr-2.0.4/bin/idr --samples YJM789-ATAC-Rep1/YJM789-ATAC-Rep1.2x50mers.sacCer3_updated.noInDels.bowtie.unique.dedup.MACS-2.1.0.p1e-1_peaks.narrowPeak YJM789-ATAC-Rep2/YJM789-ATAC-Rep2.2x50mers.sacCer3_updated.noInDels.bowtie.unique.dedup.MACS-2.1.0.p1e-1_peaks.narrowPeak --input-file-type narrowPeak --rank signal.value --soft-idr-threshold 0.05 --plot --use-best-multisummit-IDR --peak-list YJM789-ATAC.2x50mers.sacCer3_updated.noInDels.bowtie.unique.dedup.merged.sorted.MACS-2.1.0.p1e-1_peaks.narrowPeak --output-file YJM789-ATAC-Rep1-vs-YJM789-ATAC-Rep2.2x50mers.sacCer3_updated.noInDels.bowtie.unique.dedup.ind-reps.MACS2.IDR
module load python/3.6.1; /oak/stanford/groups/akundaje/marinovg/programs/idr-2.0.4/bin/idr --samples AWRI1631-ATAC.2x36mers.sacCer3_updated.noInDels.bowtie.unique.dedup.merged.sorted.pseudoRep1.MACS-2.1.0.p1e-1_peaks.narrowPeak AWRI1631-ATAC.2x36mers.sacCer3_updated.noInDels.bowtie.unique.dedup.merged.sorted.pseudoRep2.MACS-2.1.0.p1e-1_peaks.narrowPeak --input-file-type narrowPeak --rank p.value --soft-idr-threshold 0.05 --plot --use-best-multisummit-IDR --peak-list AWRI1631-ATAC.2x36mers.sacCer3_updated.noInDels.bowtie.unique.dedup.merged.sorted.MACS-2.1.0.p1e-1_peaks.narrowPeak --output-file AWRI1631-ATAC.2x36mers.sacCer3_updated.noInDels.bowtie.unique.dedup.pooled.MACS2.IDR
module load python/3.6.1; /oak/stanford/groups/akundaje/marinovg/programs/idr-2.0.4/bin/idr --samples BY4741-ATAC.2x36mers.sacCer3_updated.noInDels.bowtie.unique.dedup.merged.sorted.pseudoRep1.MACS-2.1.0.p1e-1_peaks.narrowPeak BY4741-ATAC.2x36mers.sacCer3_updated.noInDels.bowtie.unique.dedup.merged.sorted.pseudoRep2.MACS-2.1.0.p1e-1_peaks.narrowPeak --input-file-type narrowPeak --rank p.value --soft-idr-threshold 0.05 --plot --use-best-multisummit-IDR --peak-list BY4741-ATAC.2x36mers.sacCer3_updated.noInDels.bowtie.unique.dedup.merged.sorted.MACS-2.1.0.p1e-1_peaks.narrowPeak --output-file BY4741-ATAC.2x36mers.sacCer3_updated.noInDels.bowtie.unique.dedup.pooled.MACS2.IDR
module load python/3.6.1; /oak/stanford/groups/akundaje/marinovg/programs/idr-2.0.4/bin/idr --samples BY4742-ATAC.2x36mers.sacCer3_updated.noInDels.bowtie.unique.dedup.merged.sorted.pseudoRep1.MACS-2.1.0.p1e-1_peaks.narrowPeak BY4742-ATAC.2x36mers.sacCer3_updated.noInDels.bowtie.unique.dedup.merged.sorted.pseudoRep2.MACS-2.1.0.p1e-1_peaks.narrowPeak --input-file-type narrowPeak --rank p.value --soft-idr-threshold 0.05 --plot --use-best-multisummit-IDR --peak-list BY4742-ATAC.2x36mers.sacCer3_updated.noInDels.bowtie.unique.dedup.merged.sorted.MACS-2.1.0.p1e-1_peaks.narrowPeak --output-file BY4742-ATAC.2x36mers.sacCer3_updated.noInDels.bowtie.unique.dedup.pooled.MACS2.IDR
module load python/3.6.1; /oak/stanford/groups/akundaje/marinovg/programs/idr-2.0.4/bin/idr --samples RM11_1a-ATAC.2x36mers.sacCer3_updated.noInDels.bowtie.unique.dedup.merged.sorted.pseudoRep1.MACS-2.1.0.p1e-1_peaks.narrowPeak RM11_1a-ATAC.2x36mers.sacCer3_updated.noInDels.bowtie.unique.dedup.merged.sorted.pseudoRep2.MACS-2.1.0.p1e-1_peaks.narrowPeak --input-file-type narrowPeak --rank p.value --soft-idr-threshold 0.05 --plot --use-best-multisummit-IDR --peak-list RM11_1a-ATAC.2x36mers.sacCer3_updated.noInDels.bowtie.unique.dedup.merged.sorted.MACS-2.1.0.p1e-1_peaks.narrowPeak --output-file RM11_1a-ATAC.2x36mers.sacCer3_updated.noInDels.bowtie.unique.dedup.pooled.MACS2.IDR
module load python/3.6.1; /oak/stanford/groups/akundaje/marinovg/programs/idr-2.0.4/bin/idr --samples YJM789-ATAC.2x36mers.sacCer3_updated.noInDels.bowtie.unique.dedup.merged.sorted.pseudoRep1.MACS-2.1.0.p1e-1_peaks.narrowPeak YJM789-ATAC.2x36mers.sacCer3_updated.noInDels.bowtie.unique.dedup.merged.sorted.pseudoRep2.MACS-2.1.0.p1e-1_peaks.narrowPeak --input-file-type narrowPeak --rank p.value --soft-idr-threshold 0.05 --plot --use-best-multisummit-IDR --peak-list YJM789-ATAC.2x36mers.sacCer3_updated.noInDels.bowtie.unique.dedup.merged.sorted.MACS-2.1.0.p1e-1_peaks.narrowPeak --output-file YJM789-ATAC.2x36mers.sacCer3_updated.noInDels.bowtie.unique.dedup.pooled.MACS2.IDR
module load python/3.6.1; /oak/stanford/groups/akundaje/marinovg/programs/idr-2.0.4/bin/idr --samples AWRI1631-ATAC-Rep1/AWRI1631-ATAC-Rep1.2x36mers.sacCer3_updated.noInDels.bowtie.unique.dedup.pseudoRep1.MACS-2.1.0.p1e-1_peaks.narrowPeak AWRI1631-ATAC-Rep1/AWRI1631-ATAC-Rep1.2x36mers.sacCer3_updated.noInDels.bowtie.unique.dedup.pseudoRep2.MACS-2.1.0.p1e-1_peaks.narrowPeak --input-file-type narrowPeak --rank p.value --soft-idr-threshold 0.05 --plot --use-best-multisummit-IDR --peak-list AWRI1631-ATAC-Rep1/AWRI1631-ATAC-Rep1.2x36mers.sacCer3_updated.noInDels.bowtie.unique.dedup.MACS-2.1.0.p1e-1_peaks.narrowPeak --output-file AWRI1631-ATAC-Rep1/AWRI1631-ATAC-Rep1.2x36mers.sacCer3_updated.noInDels.bowtie.unique.dedup.ind_pseudo_rep.MACS2.IDR
module load python/3.6.1; /oak/stanford/groups/akundaje/marinovg/programs/idr-2.0.4/bin/idr --samples AWRI1631-ATAC-Rep2/AWRI1631-ATAC-Rep2.2x36mers.sacCer3_updated.noInDels.bowtie.unique.dedup.pseudoRep1.MACS-2.1.0.p1e-1_peaks.narrowPeak AWRI1631-ATAC-Rep2/AWRI1631-ATAC-Rep2.2x36mers.sacCer3_updated.noInDels.bowtie.unique.dedup.pseudoRep2.MACS-2.1.0.p1e-1_peaks.narrowPeak --input-file-type narrowPeak --rank p.value --soft-idr-threshold 0.05 --plot --use-best-multisummit-IDR --peak-list AWRI1631-ATAC-Rep2/AWRI1631-ATAC-Rep2.2x36mers.sacCer3_updated.noInDels.bowtie.unique.dedup.MACS-2.1.0.p1e-1_peaks.narrowPeak --output-file AWRI1631-ATAC-Rep2/AWRI1631-ATAC-Rep2.2x36mers.sacCer3_updated.noInDels.bowtie.unique.dedup.ind_pseudo_rep.MACS2.IDR
module load python/3.6.1; /oak/stanford/groups/akundaje/marinovg/programs/idr-2.0.4/bin/idr --samples BY4741-ATAC-Rep1/BY4741-ATAC-Rep1.2x36mers.sacCer3_updated.noInDels.bowtie.unique.dedup.pseudoRep1.MACS-2.1.0.p1e-1_peaks.narrowPeak BY4741-ATAC-Rep1/BY4741-ATAC-Rep1.2x36mers.sacCer3_updated.noInDels.bowtie.unique.dedup.pseudoRep2.MACS-2.1.0.p1e-1_peaks.narrowPeak --input-file-type narrowPeak --rank p.value --soft-idr-threshold 0.05 --plot --use-best-multisummit-IDR --peak-list BY4741-ATAC-Rep1/BY4741-ATAC-Rep1.2x36mers.sacCer3_updated.noInDels.bowtie.unique.dedup.MACS-2.1.0.p1e-1_peaks.narrowPeak --output-file BY4741-ATAC-Rep1/BY4741-ATAC-Rep1.2x36mers.sacCer3_updated.noInDels.bowtie.unique.dedup.ind_pseudo_rep.MACS2.IDR
module load python/3.6.1; /oak/stanford/groups/akundaje/marinovg/programs/idr-2.0.4/bin/idr --samples BY4741-ATAC-Rep2/BY4741-ATAC-Rep2.2x36mers.sacCer3_updated.noInDels.bowtie.unique.dedup.pseudoRep1.MACS-2.1.0.p1e-1_peaks.narrowPeak BY4741-ATAC-Rep2/BY4741-ATAC-Rep2.2x36mers.sacCer3_updated.noInDels.bowtie.unique.dedup.pseudoRep2.MACS-2.1.0.p1e-1_peaks.narrowPeak --input-file-type narrowPeak --rank p.value --soft-idr-threshold 0.05 --plot --use-best-multisummit-IDR --peak-list BY4741-ATAC-Rep2/BY4741-ATAC-Rep2.2x36mers.sacCer3_updated.noInDels.bowtie.unique.dedup.MACS-2.1.0.p1e-1_peaks.narrowPeak --output-file BY4741-ATAC-Rep2/BY4741-ATAC-Rep2.2x36mers.sacCer3_updated.noInDels.bowtie.unique.dedup.ind_pseudo_rep.MACS2.IDR
module load python/3.6.1; /oak/stanford/groups/akundaje/marinovg/programs/idr-2.0.4/bin/idr --samples BY4742-ATAC-Rep1/BY4742-ATAC-Rep1.2x36mers.sacCer3_updated.noInDels.bowtie.unique.dedup.pseudoRep1.MACS-2.1.0.p1e-1_peaks.narrowPeak BY4742-ATAC-Rep1/BY4742-ATAC-Rep1.2x36mers.sacCer3_updated.noInDels.bowtie.unique.dedup.pseudoRep2.MACS-2.1.0.p1e-1_peaks.narrowPeak --input-file-type narrowPeak --rank p.value --soft-idr-threshold 0.05 --plot --use-best-multisummit-IDR --peak-list BY4742-ATAC-Rep1/BY4742-ATAC-Rep1.2x36mers.sacCer3_updated.noInDels.bowtie.unique.dedup.MACS-2.1.0.p1e-1_peaks.narrowPeak --output-file BY4742-ATAC-Rep1/BY4742-ATAC-Rep1.2x36mers.sacCer3_updated.noInDels.bowtie.unique.dedup.ind_pseudo_rep.MACS2.IDR
module load python/3.6.1; /oak/stanford/groups/akundaje/marinovg/programs/idr-2.0.4/bin/idr --samples BY4742-ATAC-Rep2/BY4742-ATAC-Rep2.2x36mers.sacCer3_updated.noInDels.bowtie.unique.dedup.pseudoRep1.MACS-2.1.0.p1e-1_peaks.narrowPeak BY4742-ATAC-Rep2/BY4742-ATAC-Rep2.2x36mers.sacCer3_updated.noInDels.bowtie.unique.dedup.pseudoRep2.MACS-2.1.0.p1e-1_peaks.narrowPeak --input-file-type narrowPeak --rank p.value --soft-idr-threshold 0.05 --plot --use-best-multisummit-IDR --peak-list BY4742-ATAC-Rep2/BY4742-ATAC-Rep2.2x36mers.sacCer3_updated.noInDels.bowtie.unique.dedup.MACS-2.1.0.p1e-1_peaks.narrowPeak --output-file BY4742-ATAC-Rep2/BY4742-ATAC-Rep2.2x36mers.sacCer3_updated.noInDels.bowtie.unique.dedup.ind_pseudo_rep.MACS2.IDR
module load python/3.6.1; /oak/stanford/groups/akundaje/marinovg/programs/idr-2.0.4/bin/idr --samples RM11_1a-ATAC-Rep1/RM11_1a-ATAC-Rep1.2x36mers.sacCer3_updated.noInDels.bowtie.unique.dedup.pseudoRep1.MACS-2.1.0.p1e-1_peaks.narrowPeak RM11_1a-ATAC-Rep1/RM11_1a-ATAC-Rep1.2x36mers.sacCer3_updated.noInDels.bowtie.unique.dedup.pseudoRep2.MACS-2.1.0.p1e-1_peaks.narrowPeak --input-file-type narrowPeak --rank p.value --soft-idr-threshold 0.05 --plot --use-best-multisummit-IDR --peak-list RM11_1a-ATAC-Rep1/RM11_1a-ATAC-Rep1.2x36mers.sacCer3_updated.noInDels.bowtie.unique.dedup.MACS-2.1.0.p1e-1_peaks.narrowPeak --output-file RM11_1a-ATAC-Rep1/RM11_1a-ATAC-Rep1.2x36mers.sacCer3_updated.noInDels.bowtie.unique.dedup.ind_pseudo_rep.MACS2.IDR
module load python/3.6.1; /oak/stanford/groups/akundaje/marinovg/programs/idr-2.0.4/bin/idr --samples RM11_1a-ATAC-Rep2/RM11_1a-ATAC-Rep2.2x36mers.sacCer3_updated.noInDels.bowtie.unique.dedup.pseudoRep1.MACS-2.1.0.p1e-1_peaks.narrowPeak RM11_1a-ATAC-Rep2/RM11_1a-ATAC-Rep2.2x36mers.sacCer3_updated.noInDels.bowtie.unique.dedup.pseudoRep2.MACS-2.1.0.p1e-1_peaks.narrowPeak --input-file-type narrowPeak --rank p.value --soft-idr-threshold 0.05 --plot --use-best-multisummit-IDR --peak-list RM11_1a-ATAC-Rep2/RM11_1a-ATAC-Rep2.2x36mers.sacCer3_updated.noInDels.bowtie.unique.dedup.MACS-2.1.0.p1e-1_peaks.narrowPeak --output-file RM11_1a-ATAC-Rep2/RM11_1a-ATAC-Rep2.2x36mers.sacCer3_updated.noInDels.bowtie.unique.dedup.ind_pseudo_rep.MACS2.IDR
module load python/3.6.1; /oak/stanford/groups/akundaje/marinovg/programs/idr-2.0.4/bin/idr --samples YJM789-ATAC-Rep1/YJM789-ATAC-Rep1.2x36mers.sacCer3_updated.noInDels.bowtie.unique.dedup.pseudoRep1.MACS-2.1.0.p1e-1_peaks.narrowPeak YJM789-ATAC-Rep1/YJM789-ATAC-Rep1.2x36mers.sacCer3_updated.noInDels.bowtie.unique.dedup.pseudoRep2.MACS-2.1.0.p1e-1_peaks.narrowPeak --input-file-type narrowPeak --rank p.value --soft-idr-threshold 0.05 --plot --use-best-multisummit-IDR --peak-list YJM789-ATAC-Rep1/YJM789-ATAC-Rep1.2x36mers.sacCer3_updated.noInDels.bowtie.unique.dedup.MACS-2.1.0.p1e-1_peaks.narrowPeak --output-file YJM789-ATAC-Rep1/YJM789-ATAC-Rep1.2x36mers.sacCer3_updated.noInDels.bowtie.unique.dedup.ind_pseudo_rep.MACS2.IDR
module load python/3.6.1; /oak/stanford/groups/akundaje/marinovg/programs/idr-2.0.4/bin/idr --samples YJM789-ATAC-Rep2/YJM789-ATAC-Rep2.2x36mers.sacCer3_updated.noInDels.bowtie.unique.dedup.pseudoRep1.MACS-2.1.0.p1e-1_peaks.narrowPeak YJM789-ATAC-Rep2/YJM789-ATAC-Rep2.2x36mers.sacCer3_updated.noInDels.bowtie.unique.dedup.pseudoRep2.MACS-2.1.0.p1e-1_peaks.narrowPeak --input-file-type narrowPeak --rank p.value --soft-idr-threshold 0.05 --plot --use-best-multisummit-IDR --peak-list YJM789-ATAC-Rep2/YJM789-ATAC-Rep2.2x36mers.sacCer3_updated.noInDels.bowtie.unique.dedup.MACS-2.1.0.p1e-1_peaks.narrowPeak --output-file YJM789-ATAC-Rep2/YJM789-ATAC-Rep2.2x36mers.sacCer3_updated.noInDels.bowtie.unique.dedup.ind_pseudo_rep.MACS2.IDR
module load python/3.6.1; /oak/stanford/groups/akundaje/marinovg/programs/idr-2.0.4/bin/idr --samples AWRI1631-ATAC-Rep1/AWRI1631-ATAC-Rep1.2x36mers.sacCer3_updated.noInDels.bowtie.unique.dedup.MACS-2.1.0.p1e-1_peaks.narrowPeak AWRI1631-ATAC-Rep2/AWRI1631-ATAC-Rep2.2x36mers.sacCer3_updated.noInDels.bowtie.unique.dedup.MACS-2.1.0.p1e-1_peaks.narrowPeak --input-file-type narrowPeak --rank signal.value --soft-idr-threshold 0.05 --plot --use-best-multisummit-IDR --peak-list AWRI1631-ATAC.2x36mers.sacCer3_updated.noInDels.bowtie.unique.dedup.merged.sorted.MACS-2.1.0.p1e-1_peaks.narrowPeak --output-file AWRI1631-ATAC-Rep1-vs-AWRI1631-ATAC-Rep2.2x36mers.sacCer3_updated.noInDels.bowtie.unique.dedup.ind-reps.MACS2.IDR
module load python/3.6.1; /oak/stanford/groups/akundaje/marinovg/programs/idr-2.0.4/bin/idr --samples BY4741-ATAC-Rep1/BY4741-ATAC-Rep1.2x36mers.sacCer3_updated.noInDels.bowtie.unique.dedup.MACS-2.1.0.p1e-1_peaks.narrowPeak BY4741-ATAC-Rep2/BY4741-ATAC-Rep2.2x36mers.sacCer3_updated.noInDels.bowtie.unique.dedup.MACS-2.1.0.p1e-1_peaks.narrowPeak --input-file-type narrowPeak --rank signal.value --soft-idr-threshold 0.05 --plot --use-best-multisummit-IDR --peak-list BY4741-ATAC.2x36mers.sacCer3_updated.noInDels.bowtie.unique.dedup.merged.sorted.MACS-2.1.0.p1e-1_peaks.narrowPeak --output-file BY4741-ATAC-Rep1-vs-BY4741-ATAC-Rep2.2x36mers.sacCer3_updated.noInDels.bowtie.unique.dedup.ind-reps.MACS2.IDR
module load python/3.6.1; /oak/stanford/groups/akundaje/marinovg/programs/idr-2.0.4/bin/idr --samples BY4742-ATAC-Rep1/BY4742-ATAC-Rep1.2x36mers.sacCer3_updated.noInDels.bowtie.unique.dedup.MACS-2.1.0.p1e-1_peaks.narrowPeak BY4742-ATAC-Rep2/BY4742-ATAC-Rep2.2x36mers.sacCer3_updated.noInDels.bowtie.unique.dedup.MACS-2.1.0.p1e-1_peaks.narrowPeak --input-file-type narrowPeak --rank signal.value --soft-idr-threshold 0.05 --plot --use-best-multisummit-IDR --peak-list BY4742-ATAC.2x36mers.sacCer3_updated.noInDels.bowtie.unique.dedup.merged.sorted.MACS-2.1.0.p1e-1_peaks.narrowPeak --output-file BY4742-ATAC-Rep1-vs-BY4742-ATAC-Rep2.2x36mers.sacCer3_updated.noInDels.bowtie.unique.dedup.ind-reps.MACS2.IDR
module load python/3.6.1; /oak/stanford/groups/akundaje/marinovg/programs/idr-2.0.4/bin/idr --samples RM11_1a-ATAC-Rep1/RM11_1a-ATAC-Rep1.2x36mers.sacCer3_updated.noInDels.bowtie.unique.dedup.MACS-2.1.0.p1e-1_peaks.narrowPeak RM11_1a-ATAC-Rep2/RM11_1a-ATAC-Rep2.2x36mers.sacCer3_updated.noInDels.bowtie.unique.dedup.MACS-2.1.0.p1e-1_peaks.narrowPeak --input-file-type narrowPeak --rank signal.value --soft-idr-threshold 0.05 --plot --use-best-multisummit-IDR --peak-list RM11_1a-ATAC.2x36mers.sacCer3_updated.noInDels.bowtie.unique.dedup.merged.sorted.MACS-2.1.0.p1e-1_peaks.narrowPeak --output-file RM11_1a-ATAC-Rep1-vs-RM11_1a-ATAC-Rep2.2x36mers.sacCer3_updated.noInDels.bowtie.unique.dedup.ind-reps.MACS2.IDR
module load python/3.6.1; /oak/stanford/groups/akundaje/marinovg/programs/idr-2.0.4/bin/idr --samples YJM789-ATAC-Rep1/YJM789-ATAC-Rep1.2x36mers.sacCer3_updated.noInDels.bowtie.unique.dedup.MACS-2.1.0.p1e-1_peaks.narrowPeak YJM789-ATAC-Rep2/YJM789-ATAC-Rep2.2x36mers.sacCer3_updated.noInDels.bowtie.unique.dedup.MACS-2.1.0.p1e-1_peaks.narrowPeak --input-file-type narrowPeak --rank signal.value --soft-idr-threshold 0.05 --plot --use-best-multisummit-IDR --peak-list YJM789-ATAC.2x36mers.sacCer3_updated.noInDels.bowtie.unique.dedup.merged.sorted.MACS-2.1.0.p1e-1_peaks.narrowPeak --output-file YJM789-ATAC-Rep1-vs-YJM789-ATAC-Rep2.2x36mers.sacCer3_updated.noInDels.bowtie.unique.dedup.ind-reps.MACS2.IDR