module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=L5010-HEK_GFP_1_Input.2x36mers.unique.bam OUTPUT=L5010-HEK_GFP_1_Input.2x36mers.unique.dedup.bam METRICS_FILE=L5010-HEK_GFP_1_Input.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=L5040-HEK_GFP_1_SPI_ChIP.2x36mers.unique.bam OUTPUT=L5040-HEK_GFP_1_SPI_ChIP.2x36mers.unique.dedup.bam METRICS_FILE=L5040-HEK_GFP_1_SPI_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=L5041-HEK_SPI1_1_SPI_ChIP.2x36mers.unique.bam OUTPUT=L5041-HEK_SPI1_1_SPI_ChIP.2x36mers.unique.dedup.bam METRICS_FILE=L5041-HEK_SPI1_1_SPI_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=L5042-HEK_SPI1_0.75_SPI_ChIP.2x36mers.unique.bam OUTPUT=L5042-HEK_SPI1_0.75_SPI_ChIP.2x36mers.unique.dedup.bam METRICS_FILE=L5042-HEK_SPI1_0.75_SPI_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=L5043-HEK_SPI1_0.5_SPI_ChIP.2x36mers.unique.bam OUTPUT=L5043-HEK_SPI1_0.5_SPI_ChIP.2x36mers.unique.dedup.bam METRICS_FILE=L5043-HEK_SPI1_0.5_SPI_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=L5044-HEK_SPI1_0.25_SPI_ChIP.2x36mers.unique.bam OUTPUT=L5044-HEK_SPI1_0.25_SPI_ChIP.2x36mers.unique.dedup.bam METRICS_FILE=L5044-HEK_SPI1_0.25_SPI_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=L5045-HEK_SPI1_0.05_SPI_ChIP.2x36mers.unique.bam OUTPUT=L5045-HEK_SPI1_0.05_SPI_ChIP.2x36mers.unique.dedup.bam METRICS_FILE=L5045-HEK_SPI1_0.05_SPI_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=L5046-HEK_SOX2_1_SOX_ChIP.2x36mers.unique.bam OUTPUT=L5046-HEK_SOX2_1_SOX_ChIP.2x36mers.unique.dedup.bam METRICS_FILE=L5046-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=L5047-HEK_SOX2_0.75_SOX_ChIP.2x36mers.unique.bam OUTPUT=L5047-HEK_SOX2_0.75_SOX_ChIP.2x36mers.unique.dedup.bam METRICS_FILE=L5047-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=L5048-HEK_SOX2_0.5_SOX_ChIP.2x36mers.unique.bam OUTPUT=L5048-HEK_SOX2_0.5_SOX_ChIP.2x36mers.unique.dedup.bam METRICS_FILE=L5048-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=L5049-HEK_SOX2_0.25_SOX_ChIP.2x36mers.unique.bam OUTPUT=L5049-HEK_SOX2_0.25_SOX_ChIP.2x36mers.unique.dedup.bam METRICS_FILE=L5049-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=L5050-HEK_SOX2_0.05_SOX_ChIP.2x36mers.unique.bam OUTPUT=L5050-HEK_SOX2_0.05_SOX_ChIP.2x36mers.unique.dedup.bam METRICS_FILE=L5050-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=L5051-HEK_IRF4_1_IRF4_ChIP.2x36mers.unique.bam OUTPUT=L5051-HEK_IRF4_1_IRF4_ChIP.2x36mers.unique.dedup.bam METRICS_FILE=L5051-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=L5052-HEK_IRF4_0.75_IRF4_ChIP.2x36mers.unique.bam OUTPUT=L5052-HEK_IRF4_0.75_IRF4_ChIP.2x36mers.unique.dedup.bam METRICS_FILE=L5052-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=L5053-HEK_IRF4_0.5_IRF4_ChIP.2x36mers.unique.bam OUTPUT=L5053-HEK_IRF4_0.5_IRF4_ChIP.2x36mers.unique.dedup.bam METRICS_FILE=L5053-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=L5054-HEK_IRF4_0.25_IRF4_ChIP.2x36mers.unique.bam OUTPUT=L5054-HEK_IRF4_0.25_IRF4_ChIP.2x36mers.unique.dedup.bam METRICS_FILE=L5054-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=L5055-HEK_IRF4_0.05_IRF4_ChIP.2x36mers.unique.bam OUTPUT=L5055-HEK_IRF4_0.05_IRF4_ChIP.2x36mers.unique.dedup.bam METRICS_FILE=L5055-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=L5056-HEK_LEF1_1_LEF1_ChIP.2x36mers.unique.bam OUTPUT=L5056-HEK_LEF1_1_LEF1_ChIP.2x36mers.unique.dedup.bam METRICS_FILE=L5056-HEK_LEF1_1_LEF1_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=L5057-HEK_LEF1_0.75_LEF1_ChIP.2x36mers.unique.bam OUTPUT=L5057-HEK_LEF1_0.75_LEF1_ChIP.2x36mers.unique.dedup.bam METRICS_FILE=L5057-HEK_LEF1_0.75_LEF1_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=L5058-HEK_LEF1_0.5_LEF1_ChIP.2x36mers.unique.bam OUTPUT=L5058-HEK_LEF1_0.5_LEF1_ChIP.2x36mers.unique.dedup.bam METRICS_FILE=L5058-HEK_LEF1_0.5_LEF1_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=L5059-HEK_LEF1_0.25_LEF1_ChIP.2x36mers.unique.bam OUTPUT=L5059-HEK_LEF1_0.25_LEF1_ChIP.2x36mers.unique.dedup.bam METRICS_FILE=L5059-HEK_LEF1_0.25_LEF1_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=L5060-HEK_LEF1_0.05_LEF1_ChIP.2x36mers.unique.bam OUTPUT=L5060-HEK_LEF1_0.05_LEF1_ChIP.2x36mers.unique.dedup.bam METRICS_FILE=L5060-HEK_LEF1_0.05_LEF1_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=L5061-HEK_ALX4_1_ALX4-FLAG_ChIP.2x36mers.unique.bam OUTPUT=L5061-HEK_ALX4_1_ALX4-FLAG_ChIP.2x36mers.unique.dedup.bam METRICS_FILE=L5061-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=L5062-HEK_ALX4_0.75_ALX4-FLAG_ChIP.2x36mers.unique.bam OUTPUT=L5062-HEK_ALX4_0.75_ALX4-FLAG_ChIP.2x36mers.unique.dedup.bam METRICS_FILE=L5062-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=L5063-HEK_ALX4_0.5_ALX4-FLAG_ChIP.2x36mers.unique.bam OUTPUT=L5063-HEK_ALX4_0.5_ALX4-FLAG_ChIP.2x36mers.unique.dedup.bam METRICS_FILE=L5063-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=L5064-HEK_ALX4_0.25_ALX4-FLAG_ChIP.2x36mers.unique.bam OUTPUT=L5064-HEK_ALX4_0.25_ALX4-FLAG_ChIP.2x36mers.unique.dedup.bam METRICS_FILE=L5064-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=L5065-HEK_ALX4_0.05_ALX4-FLAG_ChIP.2x36mers.unique.bam OUTPUT=L5065-HEK_ALX4_0.05_ALX4-FLAG_ChIP.2x36mers.unique.dedup.bam METRICS_FILE=L5065-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=L5066-HEK_SOX_ChIP.2x36mers.unique.bam OUTPUT=L5066-HEK_SOX_ChIP.2x36mers.unique.dedup.bam METRICS_FILE=L5066-HEK_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=L5067-HEK_IRF4_ChIP.2x36mers.unique.bam OUTPUT=L5067-HEK_IRF4_ChIP.2x36mers.unique.dedup.bam METRICS_FILE=L5067-HEK_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=L5068-HEK_LEF1_ChIP.2x36mers.unique.bam OUTPUT=L5068-HEK_LEF1_ChIP.2x36mers.unique.dedup.bam METRICS_FILE=L5068-HEK_LEF1_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=L5069-HEK_ALX4-FLAG_ChIP.2x36mers.unique.bam OUTPUT=L5069-HEK_ALX4-FLAG_ChIP.2x36mers.unique.dedup.bam METRICS_FILE=L5069-HEK_ALX4-FLAG_ChIP.2x36mers.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true