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-SPP-300K/BCL6_FA_ChIP-seq-GSM2754207.36mers.unique.dedup.pseudoRep1_VS_FA_IgG_control-GSM2754209.36mers.unique.dedup.pseudoRep1.narrowPeak.gz BCL6_FA_ChIP-seq-GSM2754207-vs-FA_IgG_control-GSM2754209.dedup.pseudoRep2-SPP-300K/BCL6_FA_ChIP-seq-GSM2754207.36mers.unique.dedup.pseudoRep2_VS_FA_IgG_control-GSM2754209.36mers.unique.dedup.pseudoRep2.narrowPeak.gz --input-file-type narrowPeak --output-file SPP-IDR-BCL6_FA_ChIP-seq-GSM2754207-vs-FA_IgG_control-GSM2754209-indpseudoreps --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 BCL6_FA_ChIP-seq-GSM2754207-vs-FA_input_DNA-GSM2754208.dedup.pseudoRep1-SPP-300K/BCL6_FA_ChIP-seq-GSM2754207.36mers.unique.dedup.pseudoRep1_VS_FA_input_DNA-GSM2754208.36mers.unique.dedup.pseudoRep1.narrowPeak.gz BCL6_FA_ChIP-seq-GSM2754207-vs-FA_input_DNA-GSM2754208.dedup.pseudoRep2-SPP-300K/BCL6_FA_ChIP-seq-GSM2754207.36mers.unique.dedup.pseudoRep2_VS_FA_input_DNA-GSM2754208.36mers.unique.dedup.pseudoRep2.narrowPeak.gz --input-file-type narrowPeak --output-file SPP-IDR-BCL6_FA_ChIP-seq-GSM2754207-vs-FA_input_DNA-GSM2754208-indpseudoreps --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 BCL6_UV-ChIP-seq_merged-vs-minusUV_control_ChIP-GSM2754206.dedup.pseudoRep1-SPP-300K/BCL6_UV-ChIP-seq_merged.36mers.unique.dedup.pseudoRep1_VS_minusUV_control_ChIP-GSM2754206.36mers.unique.dedup.pseudoRep1.narrowPeak.gz BCL6_UV-ChIP-seq_merged-vs-minusUV_control_ChIP-GSM2754206.dedup.pseudoRep2-SPP-300K/BCL6_UV-ChIP-seq_merged.36mers.unique.dedup.pseudoRep2_VS_minusUV_control_ChIP-GSM2754206.36mers.unique.dedup.pseudoRep2.narrowPeak.gz --input-file-type narrowPeak --output-file SPP-IDR-BCL6_UV-ChIP-seq_merged-vs-minusUV_control-pseudoreps --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 BCL6_UV-ChIP-seq_merged-vs-UV_IgG_control-GSM2754205.dedup.pseudoRep1-SPP-300K/BCL6_UV-ChIP-seq_merged.36mers.unique.dedup.pseudoRep1_VS_UV_IgG_control-GSM2754205.36mers.unique.dedup.pseudoRep1.narrowPeak.gz BCL6_UV-ChIP-seq_merged-vs-UV_IgG_control-GSM2754205.dedup.pseudoRep2-SPP-300K/BCL6_UV-ChIP-seq_merged.36mers.unique.dedup.pseudoRep2_VS_UV_IgG_control-GSM2754205.36mers.unique.dedup.pseudoRep2.narrowPeak.gz --input-file-type narrowPeak --output-file SPP-IDR-BCL6_UV-ChIP-seq_merged-vs-UV_IgG_control-GSM2754205-pseudoreps --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 BCL6_UV-ChIP-seq_merged-vs-UV_input_DNA-GSM2754204.dedup.pseudoRep1-SPP-300K/BCL6_UV-ChIP-seq_merged.36mers.unique.dedup.pseudoRep1_VS_UV_input_DNA-GSM2754204.36mers.unique.dedup.pseudoRep1.narrowPeak.gz BCL6_UV-ChIP-seq_merged-vs-UV_input_DNA-GSM2754204.dedup.pseudoRep2-SPP-300K/BCL6_UV-ChIP-seq_merged.36mers.unique.dedup.pseudoRep2_VS_UV_input_DNA-GSM2754204.36mers.unique.dedup.pseudoRep2.narrowPeak.gz --input-file-type narrowPeak --output-file SPP-IDR-BCL6_UV-ChIP-seq_merged-vs-UV_input_DNA-GSM2754204-pseudoreps --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 BCL6_UV-ChIP-seq_repl1-GSM2754202-vs-minusUV_control_ChIP-GSM2754206.dedup-SPP-300K/BCL6_UV-ChIP-seq_repl1-GSM2754202.36mers.unique.dedup_VS_minusUV_control_ChIP-GSM2754206.36mers.unique.dedup.narrowPeak.gz BCL6_UV-ChIP-seq_repl2-GSM2754203-vs-minusUV_control_ChIP-GSM2754206.dedup-SPP-300K/BCL6_UV-ChIP-seq_repl2-GSM2754203.36mers.unique.dedup_VS_minusUV_control_ChIP-GSM2754206.36mers.unique.dedup.narrowPeak.gz --input-file-type narrowPeak --output-file SPP-IDR-BCL6_UV-ChIP-seq_repl2-GSM2754203-vs-minusUV_control_ChIP-GSM2754206-indreps --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 BCL6_UV-ChIP-seq_repl1-GSM2754202-vs-UV_IgG_control-GSM2754205.dedup-SPP-300K/BCL6_UV-ChIP-seq_repl1-GSM2754202.36mers.unique.dedup_VS_UV_IgG_control-GSM2754205.36mers.unique.dedup.narrowPeak.gz BCL6_UV-ChIP-seq_repl2-GSM2754203-vs-UV_IgG_control-GSM2754205.dedup-SPP-300K/BCL6_UV-ChIP-seq_repl2-GSM2754203.36mers.unique.dedup_VS_UV_IgG_control-GSM2754205.36mers.unique.dedup.narrowPeak.gz --input-file-type narrowPeak --output-file SPP-IDR-BCL6_UV-ChIP-seq_repl2-GSM2754203-vs-UV_IgG_control-GSM2754205-indreps --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 BCL6_UV-ChIP-seq_repl1-GSM2754202-vs-UV_input_DNA-GSM2754204.dedup-SPP-300K/BCL6_UV-ChIP-seq_repl1-GSM2754202.36mers.unique.dedup_VS_UV_input_DNA-GSM2754204.36mers.unique.dedup.narrowPeak.gz BCL6_UV-ChIP-seq_repl2-GSM2754203-vs-UV_input_DNA-GSM2754204.dedup-SPP-300K/BCL6_UV-ChIP-seq_repl2-GSM2754203.36mers.unique.dedup_VS_UV_input_DNA-GSM2754204.36mers.unique.dedup.narrowPeak.gz --input-file-type narrowPeak --output-file SPP-IDR-BCL6_UV-ChIP-seq_repl2-GSM2754203-vs-UV_input_DNA-GSM2754204-indreps --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 GSE29282-OCI-LY1_BCL6_D-8_CHIP-GSM763404.36mers.unique.dedup.pseudoRep1-SPP-300K/GSE29282-OCI-LY1_BCL6_D-8_CHIP-GSM763404.36mers.unique.dedup.pseudoRep1_VS_GSE29282-OCI-LY1_BCL6_D-8_INPUT-GSM763405.36mers.unique.dedup.pseudoRep1.narrowPeak.gz GSE29282-OCI-LY1_BCL6_D-8_CHIP-GSM763404.36mers.unique.dedup.pseudoRep2-SPP-300K/GSE29282-OCI-LY1_BCL6_D-8_CHIP-GSM763404.36mers.unique.dedup.pseudoRep2_VS_GSE29282-OCI-LY1_BCL6_D-8_INPUT-GSM763405.36mers.unique.dedup.pseudoRep2.narrowPeak.gz --input-file-type narrowPeak --output-file SPP-IDR-GSE29282-OCI-LY1_BCL6_D-8_CHIP-GSM763404-indpseudoreps --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 GSE29282-OCI-LY1_BCL6_N-3_rep2_CHIP-GSM763402.36mers.unique.dedup.pseudoRep1-SPP-300K/GSE29282-OCI-LY1_BCL6_N-3_rep2_CHIP-GSM763402.36mers.unique.dedup.pseudoRep1_VS_GSE29282-OCI-LY1_BCL6_N-3_rep2_INPUT-GSM763403.36mers.unique.dedup.pseudoRep1.narrowPeak.gz GSE29282-OCI-LY1_BCL6_N-3_rep2_CHIP-GSM763402.36mers.unique.dedup.pseudoRep2-SPP-300K/GSE29282-OCI-LY1_BCL6_N-3_rep2_CHIP-GSM763402.36mers.unique.dedup.pseudoRep2_VS_GSE29282-OCI-LY1_BCL6_N-3_rep2_INPUT-GSM763403.36mers.unique.dedup.pseudoRep2.narrowPeak.gz --input-file-type narrowPeak --output-file SPP-IDR-GSE29282-OCI-LY1_BCL6_N-3_rep2_CHIP-GSM763402-indpseudoreps --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 GSE46663-LY1_BCL6_DMSO-GSM1133657.36mers.unique.dedup.pseudoRep1-SPP-300K/GSE46663-LY1_BCL6_DMSO-GSM1133657.36mers.unique.dedup.pseudoRep1_VS_GSE46663-LY1_WCE_DMSO-GSM1133654.36mers.unique.dedup.pseudoRep1.narrowPeak.gz GSE46663-LY1_BCL6_DMSO-GSM1133657.36mers.unique.dedup.pseudoRep2-SPP-300K/GSE46663-LY1_BCL6_DMSO-GSM1133657.36mers.unique.dedup.pseudoRep2_VS_GSE46663-LY1_WCE_DMSO-GSM1133654.36mers.unique.dedup.pseudoRep2.narrowPeak.gz --input-file-type narrowPeak --output-file SPP-IDR-GSE46663-LY1_BCL6_DMSO-GSM1133657-indpseudoreps --rank q.value --soft-idr-threshold 0.05 --plot --use-best-multisummit-IDR