module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=L6097-HEK_SOX2_1_SOX_ChIP.2x36mers.unique.bam OUTPUT=L6097-HEK_SOX2_1_SOX_ChIP.2x36mers.unique.dedup.bam METRICS_FILE=L6097-HEK_SOX2_1_SOX_ChIP.2x36mers.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=L6098-HEK_SOX2_1_SOX_ChIP.2x36mers.unique.bam OUTPUT=L6098-HEK_SOX2_1_SOX_ChIP.2x36mers.unique.dedup.bam METRICS_FILE=L6098-HEK_SOX2_1_SOX_ChIP.2x36mers.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=L6099-HEK_SOX2_0.75_SOX_ChIP.2x36mers.unique.bam OUTPUT=L6099-HEK_SOX2_0.75_SOX_ChIP.2x36mers.unique.dedup.bam METRICS_FILE=L6099-HEK_SOX2_0.75_SOX_ChIP.2x36mers.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=L6100-HEK_SOX2_0.5_SOX_ChIP.2x36mers.unique.bam OUTPUT=L6100-HEK_SOX2_0.5_SOX_ChIP.2x36mers.unique.dedup.bam METRICS_FILE=L6100-HEK_SOX2_0.5_SOX_ChIP.2x36mers.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=L6101-HEK_SOX2_0.5_SOX_ChIP.2x36mers.unique.bam OUTPUT=L6101-HEK_SOX2_0.5_SOX_ChIP.2x36mers.unique.dedup.bam METRICS_FILE=L6101-HEK_SOX2_0.5_SOX_ChIP.2x36mers.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=L6102-HEK_SOX2_0.25_SOX_ChIP.2x36mers.unique.bam OUTPUT=L6102-HEK_SOX2_0.25_SOX_ChIP.2x36mers.unique.dedup.bam METRICS_FILE=L6102-HEK_SOX2_0.25_SOX_ChIP.2x36mers.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=L6103-HEK_SOX2_0.25_SOX_ChIP.2x36mers.unique.bam OUTPUT=L6103-HEK_SOX2_0.25_SOX_ChIP.2x36mers.unique.dedup.bam METRICS_FILE=L6103-HEK_SOX2_0.25_SOX_ChIP.2x36mers.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=L6104-HEK_SOX2_0.05_SOX_ChIP.2x36mers.unique.bam OUTPUT=L6104-HEK_SOX2_0.05_SOX_ChIP.2x36mers.unique.dedup.bam METRICS_FILE=L6104-HEK_SOX2_0.05_SOX_ChIP.2x36mers.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=L6105-HEK_SOX2_0.05_SOX_ChIP.2x36mers.unique.bam OUTPUT=L6105-HEK_SOX2_0.05_SOX_ChIP.2x36mers.unique.dedup.bam METRICS_FILE=L6105-HEK_SOX2_0.05_SOX_ChIP.2x36mers.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=L6106-HEK_IRF4_1_IRF4_ChIP.2x36mers.unique.bam OUTPUT=L6106-HEK_IRF4_1_IRF4_ChIP.2x36mers.unique.dedup.bam METRICS_FILE=L6106-HEK_IRF4_1_IRF4_ChIP.2x36mers.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=L6107-HEK_IRF4_1_IRF4_ChIP.2x36mers.unique.bam OUTPUT=L6107-HEK_IRF4_1_IRF4_ChIP.2x36mers.unique.dedup.bam METRICS_FILE=L6107-HEK_IRF4_1_IRF4_ChIP.2x36mers.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=L6108-HEK_IRF4_0.75_IRF4_ChIP.2x36mers.unique.bam OUTPUT=L6108-HEK_IRF4_0.75_IRF4_ChIP.2x36mers.unique.dedup.bam METRICS_FILE=L6108-HEK_IRF4_0.75_IRF4_ChIP.2x36mers.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=L6109-HEK_IRF4_0.5_IRF4_ChIP.2x36mers.unique.bam OUTPUT=L6109-HEK_IRF4_0.5_IRF4_ChIP.2x36mers.unique.dedup.bam METRICS_FILE=L6109-HEK_IRF4_0.5_IRF4_ChIP.2x36mers.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=L6110-HEK_IRF4_0.5_IRF4_ChIP.2x36mers.unique.bam OUTPUT=L6110-HEK_IRF4_0.5_IRF4_ChIP.2x36mers.unique.dedup.bam METRICS_FILE=L6110-HEK_IRF4_0.5_IRF4_ChIP.2x36mers.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=L6111-HEK_IRF4_0.25_IRF4_ChIP.2x36mers.unique.bam OUTPUT=L6111-HEK_IRF4_0.25_IRF4_ChIP.2x36mers.unique.dedup.bam METRICS_FILE=L6111-HEK_IRF4_0.25_IRF4_ChIP.2x36mers.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=L6112-HEK_IRF4_0.25_IRF4_ChIP.2x36mers.unique.bam OUTPUT=L6112-HEK_IRF4_0.25_IRF4_ChIP.2x36mers.unique.dedup.bam METRICS_FILE=L6112-HEK_IRF4_0.25_IRF4_ChIP.2x36mers.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=L6113-HEK_IRF4_0.05_IRF4_ChIP.2x36mers.unique.bam OUTPUT=L6113-HEK_IRF4_0.05_IRF4_ChIP.2x36mers.unique.dedup.bam METRICS_FILE=L6113-HEK_IRF4_0.05_IRF4_ChIP.2x36mers.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=L6114-HEK_IRF4_0.05_IRF4_ChIP.2x36mers.unique.bam OUTPUT=L6114-HEK_IRF4_0.05_IRF4_ChIP.2x36mers.unique.dedup.bam METRICS_FILE=L6114-HEK_IRF4_0.05_IRF4_ChIP.2x36mers.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=L6115-HEK_ALX4_1_ALX4-FLAG_ChIP.2x36mers.unique.bam OUTPUT=L6115-HEK_ALX4_1_ALX4-FLAG_ChIP.2x36mers.unique.dedup.bam METRICS_FILE=L6115-HEK_ALX4_1_ALX4-FLAG_ChIP.2x36mers.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=L6116-HEK_ALX4_1_ALX4-FLAG_ChIP.2x36mers.unique.bam OUTPUT=L6116-HEK_ALX4_1_ALX4-FLAG_ChIP.2x36mers.unique.dedup.bam METRICS_FILE=L6116-HEK_ALX4_1_ALX4-FLAG_ChIP.2x36mers.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=L6117-HEK_ALX4_0.75_ALX4-FLAG_ChIP.2x36mers.unique.bam OUTPUT=L6117-HEK_ALX4_0.75_ALX4-FLAG_ChIP.2x36mers.unique.dedup.bam METRICS_FILE=L6117-HEK_ALX4_0.75_ALX4-FLAG_ChIP.2x36mers.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=L6118-HEK_ALX4_0.5_ALX4-FLAG_ChIP.2x36mers.unique.bam OUTPUT=L6118-HEK_ALX4_0.5_ALX4-FLAG_ChIP.2x36mers.unique.dedup.bam METRICS_FILE=L6118-HEK_ALX4_0.5_ALX4-FLAG_ChIP.2x36mers.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=L6119-HEK_ALX4_0.5_ALX4-FLAG_ChIP.2x36mers.unique.bam OUTPUT=L6119-HEK_ALX4_0.5_ALX4-FLAG_ChIP.2x36mers.unique.dedup.bam METRICS_FILE=L6119-HEK_ALX4_0.5_ALX4-FLAG_ChIP.2x36mers.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=L6120-HEK_ALX4_0.5_ALX4-FLAG_ChIP.2x36mers.unique.bam OUTPUT=L6120-HEK_ALX4_0.5_ALX4-FLAG_ChIP.2x36mers.unique.dedup.bam METRICS_FILE=L6120-HEK_ALX4_0.5_ALX4-FLAG_ChIP.2x36mers.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=L6121-HEK_ALX4_0.25_ALX4-FLAG_ChIP.2x36mers.unique.bam OUTPUT=L6121-HEK_ALX4_0.25_ALX4-FLAG_ChIP.2x36mers.unique.dedup.bam METRICS_FILE=L6121-HEK_ALX4_0.25_ALX4-FLAG_ChIP.2x36mers.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=L6122-HEK_ALX4_0.25_ALX4-FLAG_ChIP.2x36mers.unique.bam OUTPUT=L6122-HEK_ALX4_0.25_ALX4-FLAG_ChIP.2x36mers.unique.dedup.bam METRICS_FILE=L6122-HEK_ALX4_0.25_ALX4-FLAG_ChIP.2x36mers.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=L6123-HEK_ALX4_0.05_ALX4-FLAG_ChIP.2x36mers.unique.bam OUTPUT=L6123-HEK_ALX4_0.05_ALX4-FLAG_ChIP.2x36mers.unique.dedup.bam METRICS_FILE=L6123-HEK_ALX4_0.05_ALX4-FLAG_ChIP.2x36mers.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=L6124-HEK_ALX4_0.05_ALX4-FLAG_ChIP.2x36mers.unique.bam OUTPUT=L6124-HEK_ALX4_0.05_ALX4-FLAG_ChIP.2x36mers.unique.dedup.bam METRICS_FILE=L6124-HEK_ALX4_0.05_ALX4-FLAG_ChIP.2x36mers.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true