module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=L5770-HEK_SPI1_1_SPI_ChIP.2x36mers.unique.bam OUTPUT=L5770-HEK_SPI1_1_SPI_ChIP.2x36mers.unique.dedup.bam METRICS_FILE=L5770-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=L5771-HEK_SPI1_0.5_SPI_ChIP.2x36mers.unique.bam OUTPUT=L5771-HEK_SPI1_0.5_SPI_ChIP.2x36mers.unique.dedup.bam METRICS_FILE=L5771-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=L5772-HEK_SPI1_0.25_SPI_ChIP.2x36mers.unique.bam OUTPUT=L5772-HEK_SPI1_0.25_SPI_ChIP.2x36mers.unique.dedup.bam METRICS_FILE=L5772-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=L5773-HEK_SPI1_0.05_SPI_ChIP.2x36mers.unique.bam OUTPUT=L5773-HEK_SPI1_0.05_SPI_ChIP.2x36mers.unique.dedup.bam METRICS_FILE=L5773-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=L5774-HEK_SOX2_1_SOX_ChIP.2x36mers.unique.bam OUTPUT=L5774-HEK_SOX2_1_SOX_ChIP.2x36mers.unique.dedup.bam METRICS_FILE=L5774-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=L5775-HEK_SOX2_0.75_SOX_ChIP.2x36mers.unique.bam OUTPUT=L5775-HEK_SOX2_0.75_SOX_ChIP.2x36mers.unique.dedup.bam METRICS_FILE=L5775-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=L5776-HEK_SOX2_0.5_SOX_ChIP.2x36mers.unique.bam OUTPUT=L5776-HEK_SOX2_0.5_SOX_ChIP.2x36mers.unique.dedup.bam METRICS_FILE=L5776-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=L5777-HEK_SOX2_0.25_SOX_ChIP.2x36mers.unique.bam OUTPUT=L5777-HEK_SOX2_0.25_SOX_ChIP.2x36mers.unique.dedup.bam METRICS_FILE=L5777-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=L5778-HEK_SOX2_0.05_SOX_ChIP.2x36mers.unique.bam OUTPUT=L5778-HEK_SOX2_0.05_SOX_ChIP.2x36mers.unique.dedup.bam METRICS_FILE=L5778-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=L5779-HEK_IRF4_1_IRF4_ChIP.2x36mers.unique.bam OUTPUT=L5779-HEK_IRF4_1_IRF4_ChIP.2x36mers.unique.dedup.bam METRICS_FILE=L5779-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=L5780-HEK_IRF4_0.5_IRF4_ChIP.2x36mers.unique.bam OUTPUT=L5780-HEK_IRF4_0.5_IRF4_ChIP.2x36mers.unique.dedup.bam METRICS_FILE=L5780-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=L5781-HEK_IRF4_0.25_IRF4_ChIP.2x36mers.unique.bam OUTPUT=L5781-HEK_IRF4_0.25_IRF4_ChIP.2x36mers.unique.dedup.bam METRICS_FILE=L5781-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=L5782-HEK_IRF4_0.05_IRF4_ChIP.2x36mers.unique.bam OUTPUT=L5782-HEK_IRF4_0.05_IRF4_ChIP.2x36mers.unique.dedup.bam METRICS_FILE=L5782-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=L5783-HEK_LEF1_1_LEF1_ChIP.2x36mers.unique.bam OUTPUT=L5783-HEK_LEF1_1_LEF1_ChIP.2x36mers.unique.dedup.bam METRICS_FILE=L5783-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=L5784-HEK_LEF1_0.5_LEF1_ChIP.2x36mers.unique.bam OUTPUT=L5784-HEK_LEF1_0.5_LEF1_ChIP.2x36mers.unique.dedup.bam METRICS_FILE=L5784-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=L5785-HEK_LEF1_0.25_LEF1_ChIP.2x36mers.unique.bam OUTPUT=L5785-HEK_LEF1_0.25_LEF1_ChIP.2x36mers.unique.dedup.bam METRICS_FILE=L5785-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=L5786-HEK_LEF1_0.05_LEF1_ChIP.2x36mers.unique.bam OUTPUT=L5786-HEK_LEF1_0.05_LEF1_ChIP.2x36mers.unique.dedup.bam METRICS_FILE=L5786-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=L5787-HEK_ALX4_1_ALX4-FLAG_ChIP.2x36mers.unique.bam OUTPUT=L5787-HEK_ALX4_1_ALX4-FLAG_ChIP.2x36mers.unique.dedup.bam METRICS_FILE=L5787-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=L5788-HEK_ALX4_0.5_ALX4-FLAG_ChIP.2x36mers.unique.bam OUTPUT=L5788-HEK_ALX4_0.5_ALX4-FLAG_ChIP.2x36mers.unique.dedup.bam METRICS_FILE=L5788-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=L5789-HEK_ALX4_0.25_ALX4-FLAG_ChIP.2x36mers.unique.bam OUTPUT=L5789-HEK_ALX4_0.25_ALX4-FLAG_ChIP.2x36mers.unique.dedup.bam METRICS_FILE=L5789-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=L5790-HEK_ALX4_0.05_ALX4-FLAG_ChIP.2x36mers.unique.bam OUTPUT=L5790-HEK_ALX4_0.05_ALX4-FLAG_ChIP.2x36mers.unique.dedup.bam METRICS_FILE=L5790-HEK_ALX4_0.05_ALX4-FLAG_ChIP.2x36mers.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true