/oak/stanford/groups/akundaje/marinovg/programs/MACS-2.1.0/bin/macs2 callpeak -t BCL6_FA_ChIP-seq-GSM2754207.36mers.unique.pseudoRep1.bam -c FA_input_DNA-GSM2754208.36mers.unique.pseudoRep1.bam -n BCL6_FA_ChIP-seq-GSM2754207-vs-FA_input_DNA-GSM2754208.pseudoRep1.MACS-2.1.0.p1e-1 -g hs -f BAM --to-large -p 1e-1
/oak/stanford/groups/akundaje/marinovg/programs/MACS-2.1.0/bin/macs2 callpeak -t BCL6_FA_ChIP-seq-GSM2754207.36mers.unique.pseudoRep1.bam -c FA_IgG_control-GSM2754209.36mers.unique.pseudoRep1.bam -n BCL6_FA_ChIP-seq-GSM2754207-vs-FA_IgG_control-GSM2754209.pseudoRep1.MACS-2.1.0.p1e-1 -g hs -f BAM --to-large -p 1e-1
/oak/stanford/groups/akundaje/marinovg/programs/MACS-2.1.0/bin/macs2 callpeak -t BCL6_UV-ChIP-seq_merged.36mers.unique.pseudoRep1.bam -c UV_input_DNA-GSM2754204.36mers.unique.pseudoRep1.bam -n BCL6_UV-ChIP-seq_merged-vs-UV_input_DNA-GSM2754204.pseudoRep1.MACS-2.1.0.p1e-1 -g hs -f BAM --to-large -p 1e-1
/oak/stanford/groups/akundaje/marinovg/programs/MACS-2.1.0/bin/macs2 callpeak -t BCL6_UV-ChIP-seq_merged.36mers.unique.pseudoRep1.bam -c UV_IgG_control-GSM2754205.36mers.unique.pseudoRep1.bam -n BCL6_UV-ChIP-seq_merged-vs-UV_IgG_control-GSM2754205.pseudoRep1.MACS-2.1.0.p1e-1 -g hs -f BAM --to-large -p 1e-1
/oak/stanford/groups/akundaje/marinovg/programs/MACS-2.1.0/bin/macs2 callpeak -t BCL6_UV-ChIP-seq_merged.36mers.unique.pseudoRep1.bam -c minusUV_control_ChIP-GSM2754206.36mers.unique.pseudoRep1.bam -n BCL6_UV-ChIP-seq_merged-vs-minusUV_control_ChIP-GSM2754206.pseudoRep1.MACS-2.1.0.p1e-1 -g hs -f BAM --to-large -p 1e-1
/oak/stanford/groups/akundaje/marinovg/programs/MACS-2.1.0/bin/macs2 callpeak -t GSE29282-OCI-LY1_BCL6_D-8_CHIP-GSM763404.36mers.unique.pseudoRep1.bam -c GSE29282-OCI-LY1_BCL6_D-8_INPUT-GSM763405.36mers.unique.pseudoRep1.bam -n GSE29282-OCI-LY1_BCL6_D-8_CHIP-GSM763404.36mers.unique.pseudoRep1.pseudoRep1.MACS-2.1.0.p1e-1 -g hs -f BAM --to-large -p 1e-1
/oak/stanford/groups/akundaje/marinovg/programs/MACS-2.1.0/bin/macs2 callpeak -t GSE29282-OCI-LY1_BCL6_N-3_rep2_CHIP-GSM763402.36mers.unique.pseudoRep1.bam -c GSE29282-OCI-LY1_BCL6_N-3_rep2_INPUT-GSM763403.36mers.unique.pseudoRep1.bam -n GSE29282-OCI-LY1_BCL6_N-3_rep2_CHIP-GSM763402.36mers.unique.pseudoRep1.pseudoRep1.MACS-2.1.0.p1e-1 -g hs -f BAM --to-large -p 1e-1
/oak/stanford/groups/akundaje/marinovg/programs/MACS-2.1.0/bin/macs2 callpeak -t GSE46663-LY1_BCL6_DMSO-GSM1133657.36mers.unique.pseudoRep1.bam -c GSE46663-LY1_WCE_DMSO-GSM1133654.36mers.unique.pseudoRep1.bam -n GSE46663-LY1_BCL6_DMSO-GSM1133657.36mers.unique.pseudoRep1.pseudoRep1.MACS-2.1.0.p1e-1 -g hs -f BAM --to-large -p 1e-1
/oak/stanford/groups/akundaje/marinovg/programs/MACS-2.1.0/bin/macs2 callpeak -t BCL6_FA_ChIP-seq-GSM2754207.36mers.unique.pseudoRep2.bam -c FA_input_DNA-GSM2754208.36mers.unique.pseudoRep2.bam -n BCL6_FA_ChIP-seq-GSM2754207-vs-FA_input_DNA-GSM2754208.pseudoRep2.MACS-2.1.0.p1e-1 -g hs -f BAM --to-large -p 1e-1
/oak/stanford/groups/akundaje/marinovg/programs/MACS-2.1.0/bin/macs2 callpeak -t BCL6_FA_ChIP-seq-GSM2754207.36mers.unique.pseudoRep2.bam -c FA_IgG_control-GSM2754209.36mers.unique.pseudoRep2.bam -n BCL6_FA_ChIP-seq-GSM2754207-vs-FA_IgG_control-GSM2754209.pseudoRep2.MACS-2.1.0.p1e-1 -g hs -f BAM --to-large -p 1e-1
/oak/stanford/groups/akundaje/marinovg/programs/MACS-2.1.0/bin/macs2 callpeak -t BCL6_UV-ChIP-seq_merged.36mers.unique.pseudoRep2.bam -c UV_input_DNA-GSM2754204.36mers.unique.pseudoRep2.bam -n BCL6_UV-ChIP-seq_merged-vs-UV_input_DNA-GSM2754204.pseudoRep2.MACS-2.1.0.p1e-1 -g hs -f BAM --to-large -p 1e-1
/oak/stanford/groups/akundaje/marinovg/programs/MACS-2.1.0/bin/macs2 callpeak -t BCL6_UV-ChIP-seq_merged.36mers.unique.pseudoRep2.bam -c UV_IgG_control-GSM2754205.36mers.unique.pseudoRep2.bam -n BCL6_UV-ChIP-seq_merged-vs-UV_IgG_control-GSM2754205.pseudoRep2.MACS-2.1.0.p1e-1 -g hs -f BAM --to-large -p 1e-1
/oak/stanford/groups/akundaje/marinovg/programs/MACS-2.1.0/bin/macs2 callpeak -t BCL6_UV-ChIP-seq_merged.36mers.unique.pseudoRep2.bam -c minusUV_control_ChIP-GSM2754206.36mers.unique.pseudoRep2.bam -n BCL6_UV-ChIP-seq_merged-vs-minusUV_control_ChIP-GSM2754206.pseudoRep2.MACS-2.1.0.p1e-1 -g hs -f BAM --to-large -p 1e-1
/oak/stanford/groups/akundaje/marinovg/programs/MACS-2.1.0/bin/macs2 callpeak -t GSE29282-OCI-LY1_BCL6_D-8_CHIP-GSM763404.36mers.unique.pseudoRep2.bam -c GSE29282-OCI-LY1_BCL6_D-8_INPUT-GSM763405.36mers.unique.pseudoRep2.bam -n GSE29282-OCI-LY1_BCL6_D-8_CHIP-GSM763404.36mers.unique.pseudoRep2.pseudoRep2.MACS-2.1.0.p1e-1 -g hs -f BAM --to-large -p 1e-1
/oak/stanford/groups/akundaje/marinovg/programs/MACS-2.1.0/bin/macs2 callpeak -t GSE29282-OCI-LY1_BCL6_N-3_rep2_CHIP-GSM763402.36mers.unique.pseudoRep2.bam -c GSE29282-OCI-LY1_BCL6_N-3_rep2_INPUT-GSM763403.36mers.unique.pseudoRep2.bam -n GSE29282-OCI-LY1_BCL6_N-3_rep2_CHIP-GSM763402.36mers.unique.pseudoRep2.pseudoRep2.MACS-2.1.0.p1e-1 -g hs -f BAM --to-large -p 1e-1
/oak/stanford/groups/akundaje/marinovg/programs/MACS-2.1.0/bin/macs2 callpeak -t GSE46663-LY1_BCL6_DMSO-GSM1133657.36mers.unique.pseudoRep2.bam -c GSE46663-LY1_WCE_DMSO-GSM1133654.36mers.unique.pseudoRep2.bam -n GSE46663-LY1_BCL6_DMSO-GSM1133657.36mers.unique.pseudoRep2.pseudoRep2.MACS-2.1.0.p1e-1 -g hs -f BAM --to-large -p 1e-1
/oak/stanford/groups/akundaje/marinovg/programs/MACS-2.1.0/bin/macs2 callpeak -t BCL6_UV-ChIP-seq_repl1-GSM2754202.36mers.unique.bam -c UV_input_DNA-GSM2754204.36mers.unique.bam -n BCL6_UV-ChIP-seq_repl1-GSM2754202-vs-UV_input_DNA-GSM2754204.MACS-2.1.0.p1e-1 -g hs -f BAM --to-large -p 1e-1
/oak/stanford/groups/akundaje/marinovg/programs/MACS-2.1.0/bin/macs2 callpeak -t BCL6_UV-ChIP-seq_repl2-GSM2754203.36mers.unique.bam -c UV_input_DNA-GSM2754204.36mers.unique.bam -n BCL6_UV-ChIP-seq_repl2-GSM2754203-vs-UV_input_DNA-GSM2754204.MACS-2.1.0.p1e-1 -g hs -f BAM --to-large -p 1e-1
/oak/stanford/groups/akundaje/marinovg/programs/MACS-2.1.0/bin/macs2 callpeak -t BCL6_UV-ChIP-seq_repl1-GSM2754202.36mers.unique.bam -c UV_IgG_control-GSM2754205.36mers.unique.bam -n BCL6_UV-ChIP-seq_repl1-GSM2754202-vs-UV_IgG_control-GSM2754205.MACS-2.1.0.p1e-1 -g hs -f BAM --to-large -p 1e-1
/oak/stanford/groups/akundaje/marinovg/programs/MACS-2.1.0/bin/macs2 callpeak -t BCL6_UV-ChIP-seq_repl2-GSM2754203.36mers.unique.bam -c UV_IgG_control-GSM2754205.36mers.unique.bam -n BCL6_UV-ChIP-seq_repl2-GSM2754203-vs-UV_IgG_control-GSM2754205.MACS-2.1.0.p1e-1 -g hs -f BAM --to-large -p 1e-1
/oak/stanford/groups/akundaje/marinovg/programs/MACS-2.1.0/bin/macs2 callpeak -t BCL6_UV-ChIP-seq_repl1-GSM2754202.36mers.unique.bam -c minusUV_control_ChIP-GSM2754206.36mers.unique.bam -n BCL6_UV-ChIP-seq_repl1-GSM2754202-vs-minusUV_control_ChIP-GSM2754206.MACS-2.1.0.p1e-1 -g hs -f BAM --to-large -p 1e-1
/oak/stanford/groups/akundaje/marinovg/programs/MACS-2.1.0/bin/macs2 callpeak -t BCL6_UV-ChIP-seq_repl2-GSM2754203.36mers.unique.bam -c minusUV_control_ChIP-GSM2754206.36mers.unique.bam -n BCL6_UV-ChIP-seq_repl2-GSM2754203-vs-minusUV_control_ChIP-GSM2754206.MACS-2.1.0.p1e-1 -g hs -f BAM --to-large -p 1e-1