module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=Oct4-DamID-r1-GSM1562327.36mers.unique.bam OUTPUT=Oct4-DamID-r1-GSM1562327.36mers.unique.dedup.bam METRICS_FILE=Oct4-DamID-r1-GSM1562327.36mers.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=Oct4-DamID-r2-GSM1562328.36mers.unique.bam OUTPUT=Oct4-DamID-r2-GSM1562328.36mers.unique.dedup.bam METRICS_FILE=Oct4-DamID-r2-GSM1562328.36mers.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=GFP-DamID-r1-GSM1562329.36mers.unique.bam OUTPUT=GFP-DamID-r1-GSM1562329.36mers.unique.dedup.bam METRICS_FILE=GFP-DamID-r1-GSM1562329.36mers.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=GFP-DamID-r2-GSM1562330.36mers.unique.bam OUTPUT=GFP-DamID-r2-GSM1562330.36mers.unique.dedup.bam METRICS_FILE=GFP-DamID-r2-GSM1562330.36mers.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=Oct4-ChIPseq-shCtrl-GSM1562331.36mers.unique.bam OUTPUT=Oct4-ChIPseq-shCtrl-GSM1562331.36mers.unique.dedup.bam METRICS_FILE=Oct4-ChIPseq-shCtrl-GSM1562331.36mers.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=Oct4-ChIPseq-shNup153-2-GSM1562332.36mers.unique.bam OUTPUT=Oct4-ChIPseq-shNup153-2-GSM1562332.36mers.unique.dedup.bam METRICS_FILE=Oct4-ChIPseq-shNup153-2-GSM1562332.36mers.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=Input-ChIPseq-GSM1562338.36mers.unique.bam OUTPUT=Input-ChIPseq-GSM1562338.36mers.unique.dedup.bam METRICS_FILE=Input-ChIPseq-GSM1562338.36mers.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true