module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=WT-MS1-SCD-rep1_S7.2x36mers.unique.nochrM.bam OUTPUT=WT-MS1-SCD-rep1_S7.2x36mers.unique.nochrM.dedup.bam METRICS_FILE=WT-MS1-SCD-rep1_S7.2x36mers.unique.nochrM.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=WT-MS1-SCD-rep2_S10.2x36mers.unique.nochrM.bam OUTPUT=WT-MS1-SCD-rep2_S10.2x36mers.unique.nochrM.dedup.bam METRICS_FILE=WT-MS1-SCD-rep2_S10.2x36mers.unique.nochrM.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=WT-MS1-SCE-rep1_S1.2x36mers.unique.nochrM.bam OUTPUT=WT-MS1-SCE-rep1_S1.2x36mers.unique.nochrM.dedup.bam METRICS_FILE=WT-MS1-SCE-rep1_S1.2x36mers.unique.nochrM.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=WT-MS1-SCE-rep2_S4.2x36mers.unique.nochrM.bam OUTPUT=WT-MS1-SCE-rep2_S4.2x36mers.unique.nochrM.dedup.bam METRICS_FILE=WT-MS1-SCE-rep2_S4.2x36mers.unique.nochrM.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=Cln3-MS49-SCD-rep1_S8.2x36mers.unique.nochrM.bam OUTPUT=Cln3-MS49-SCD-rep1_S8.2x36mers.unique.nochrM.dedup.bam METRICS_FILE=Cln3-MS49-SCD-rep1_S8.2x36mers.unique.nochrM.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=Cln3-MS49-SCD-rep2_S11.2x36mers.unique.nochrM.bam OUTPUT=Cln3-MS49-SCD-rep2_S11.2x36mers.unique.nochrM.dedup.bam METRICS_FILE=Cln3-MS49-SCD-rep2_S11.2x36mers.unique.nochrM.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=Cln3-MS49-SCE-rep1_S2.2x36mers.unique.nochrM.bam OUTPUT=Cln3-MS49-SCE-rep1_S2.2x36mers.unique.nochrM.dedup.bam METRICS_FILE=Cln3-MS49-SCE-rep1_S2.2x36mers.unique.nochrM.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=Cln3-MS49-SCE-rep2_S5.2x36mers.unique.nochrM.bam OUTPUT=Cln3-MS49-SCE-rep2_S5.2x36mers.unique.nochrM.dedup.bam METRICS_FILE=Cln3-MS49-SCE-rep2_S5.2x36mers.unique.nochrM.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=Whi5-MS51-SCD-rep1_S9.2x36mers.unique.nochrM.bam OUTPUT=Whi5-MS51-SCD-rep1_S9.2x36mers.unique.nochrM.dedup.bam METRICS_FILE=Whi5-MS51-SCD-rep1_S9.2x36mers.unique.nochrM.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=Whi5-MS51-SCD-rep2_S12.2x36mers.unique.nochrM.bam OUTPUT=Whi5-MS51-SCD-rep2_S12.2x36mers.unique.nochrM.dedup.bam METRICS_FILE=Whi5-MS51-SCD-rep2_S12.2x36mers.unique.nochrM.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=Whi5-MS51-SCE-rep1_S3.2x36mers.unique.nochrM.bam OUTPUT=Whi5-MS51-SCE-rep1_S3.2x36mers.unique.nochrM.dedup.bam METRICS_FILE=Whi5-MS51-SCE-rep1_S3.2x36mers.unique.nochrM.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=Whi5-MS51-SCE-rep2_S6.2x36mers.unique.nochrM.bam OUTPUT=Whi5-MS51-SCE-rep2_S6.2x36mers.unique.nochrM.dedup.bam METRICS_FILE=Whi5-MS51-SCE-rep2_S6.2x36mers.unique.nochrM.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true