module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=BCL6_FA_ChIP-seq-GSM2754207/BCL6_FA_ChIP-seq-GSM2754207.36mers.unique.bam OUTPUT=BCL6_FA_ChIP-seq-GSM2754207.36mers.unique.dedup.bam METRICS_FILE=BCL6_FA_ChIP-seq-GSM2754207.36mers.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=BCL6_UV-ChIP-seq_merged/BCL6_UV-ChIP-seq_merged.36mers.unique.bam OUTPUT=BCL6_UV-ChIP-seq_merged.36mers.unique.dedup.bam METRICS_FILE=BCL6_UV-ChIP-seq_merged.36mers.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=BCL6_UV-ChIP-seq_repl1-GSM2754202/BCL6_UV-ChIP-seq_repl1-GSM2754202.36mers.unique.bam OUTPUT=BCL6_UV-ChIP-seq_repl1-GSM2754202.36mers.unique.dedup.bam METRICS_FILE=BCL6_UV-ChIP-seq_repl1-GSM2754202.36mers.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=BCL6_UV-ChIP-seq_repl2-GSM2754203/BCL6_UV-ChIP-seq_repl2-GSM2754203.36mers.unique.bam OUTPUT=BCL6_UV-ChIP-seq_repl2-GSM2754203.36mers.unique.dedup.bam METRICS_FILE=BCL6_UV-ChIP-seq_repl2-GSM2754203.36mers.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=FA_IgG_control-GSM2754209/FA_IgG_control-GSM2754209.36mers.unique.bam OUTPUT=FA_IgG_control-GSM2754209.36mers.unique.dedup.bam METRICS_FILE=FA_IgG_control-GSM2754209.36mers.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=FA_input_DNA-GSM2754208/FA_input_DNA-GSM2754208.36mers.unique.bam OUTPUT=FA_input_DNA-GSM2754208.36mers.unique.dedup.bam METRICS_FILE=FA_input_DNA-GSM2754208.36mers.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=GSE29282-OCI-LY1_BCL6_D-8_CHIP-GSM763404/GSE29282-OCI-LY1_BCL6_D-8_CHIP-GSM763404.36mers.unique.bam OUTPUT=GSE29282-OCI-LY1_BCL6_D-8_CHIP-GSM763404.36mers.unique.dedup.bam METRICS_FILE=GSE29282-OCI-LY1_BCL6_D-8_CHIP-GSM763404.36mers.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=GSE29282-OCI-LY1_BCL6_D-8_INPUT-GSM763405/GSE29282-OCI-LY1_BCL6_D-8_INPUT-GSM763405.36mers.unique.bam OUTPUT=GSE29282-OCI-LY1_BCL6_D-8_INPUT-GSM763405.36mers.unique.dedup.bam METRICS_FILE=GSE29282-OCI-LY1_BCL6_D-8_INPUT-GSM763405.36mers.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=GSE29282-OCI-LY1_BCL6_N-3_rep2_CHIP-GSM763402/GSE29282-OCI-LY1_BCL6_N-3_rep2_CHIP-GSM763402.36mers.unique.bam OUTPUT=GSE29282-OCI-LY1_BCL6_N-3_rep2_CHIP-GSM763402.36mers.unique.dedup.bam METRICS_FILE=GSE29282-OCI-LY1_BCL6_N-3_rep2_CHIP-GSM763402.36mers.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=GSE29282-OCI-LY1_BCL6_N-3_rep2_INPUT-GSM763403/GSE29282-OCI-LY1_BCL6_N-3_rep2_INPUT-GSM763403.36mers.unique.bam OUTPUT=GSE29282-OCI-LY1_BCL6_N-3_rep2_INPUT-GSM763403.36mers.unique.dedup.bam METRICS_FILE=GSE29282-OCI-LY1_BCL6_N-3_rep2_INPUT-GSM763403.36mers.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=GSE46663-LY1_BCL6_DMSO-GSM1133657/GSE46663-LY1_BCL6_DMSO-GSM1133657.36mers.unique.bam OUTPUT=GSE46663-LY1_BCL6_DMSO-GSM1133657.36mers.unique.dedup.bam METRICS_FILE=GSE46663-LY1_BCL6_DMSO-GSM1133657.36mers.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=GSE46663-LY1_WCE_DMSO-GSM1133654/GSE46663-LY1_WCE_DMSO-GSM1133654.36mers.unique.bam OUTPUT=GSE46663-LY1_WCE_DMSO-GSM1133654.36mers.unique.dedup.bam METRICS_FILE=GSE46663-LY1_WCE_DMSO-GSM1133654.36mers.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=minusUV_control_ChIP-GSM2754206/minusUV_control_ChIP-GSM2754206.36mers.unique.bam OUTPUT=minusUV_control_ChIP-GSM2754206.36mers.unique.dedup.bam METRICS_FILE=minusUV_control_ChIP-GSM2754206.36mers.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=UV_IgG_control-GSM2754205/UV_IgG_control-GSM2754205.36mers.unique.bam OUTPUT=UV_IgG_control-GSM2754205.36mers.unique.dedup.bam METRICS_FILE=UV_IgG_control-GSM2754205.36mers.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=UV_input_DNA-GSM2754204/UV_input_DNA-GSM2754204.36mers.unique.bam OUTPUT=UV_input_DNA-GSM2754204.36mers.unique.dedup.bam METRICS_FILE=UV_input_DNA-GSM2754204.36mers.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true