module load devel;  module load java/1.8.0_131; java -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=primary_keratinocyte-d00.PAS-seq.b1/STAR-2.5.3aAligned.sortedByCoord.out.bam OUTPUT=primary_keratinocyte-d00.PAS-seq.b1/STAR-2.5.3aAligned.sortedByCoord.out.dedup.bam METRICS_FILE=primary_keratinocyte-d00.PAS-seq.b1/STAR-2.5.3aAligned.sortedByCoord.out.dedup.mertrics CREATE_INDEX=true VALIDATION_STRINGENCY=LENIENT AS=true REMOVE_DUPLICATES=true
module load devel;  module load java/1.8.0_131; java -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=primary_keratinocyte-d00.PAS-seq.b2/STAR-2.5.3aAligned.sortedByCoord.out.bam OUTPUT=primary_keratinocyte-d00.PAS-seq.b2/STAR-2.5.3aAligned.sortedByCoord.out.dedup.bam METRICS_FILE=primary_keratinocyte-d00.PAS-seq.b2/STAR-2.5.3aAligned.sortedByCoord.out.dedup.mertrics CREATE_INDEX=true VALIDATION_STRINGENCY=LENIENT AS=true REMOVE_DUPLICATES=true
module load devel;  module load java/1.8.0_131; java -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=primary_keratinocyte-d05.PAS-seq.b1/STAR-2.5.3aAligned.sortedByCoord.out.bam OUTPUT=primary_keratinocyte-d05.PAS-seq.b1/STAR-2.5.3aAligned.sortedByCoord.out.dedup.bam METRICS_FILE=primary_keratinocyte-d05.PAS-seq.b1/STAR-2.5.3aAligned.sortedByCoord.out.dedup.mertrics CREATE_INDEX=true VALIDATION_STRINGENCY=LENIENT AS=true REMOVE_DUPLICATES=true
module load devel;  module load java/1.8.0_131; java -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=primary_keratinocyte-d05.PAS-seq.b2/STAR-2.5.3aAligned.sortedByCoord.out.bam OUTPUT=primary_keratinocyte-d05.PAS-seq.b2/STAR-2.5.3aAligned.sortedByCoord.out.dedup.bam METRICS_FILE=primary_keratinocyte-d05.PAS-seq.b2/STAR-2.5.3aAligned.sortedByCoord.out.dedup.mertrics CREATE_INDEX=true VALIDATION_STRINGENCY=LENIENT AS=true REMOVE_DUPLICATES=true
module load devel;  module load java/1.8.0_131; java -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=primary_keratinocyte-d10.PAS-seq.b1/STAR-2.5.3aAligned.sortedByCoord.out.bam OUTPUT=primary_keratinocyte-d10.PAS-seq.b1/STAR-2.5.3aAligned.sortedByCoord.out.dedup.bam METRICS_FILE=primary_keratinocyte-d10.PAS-seq.b1/STAR-2.5.3aAligned.sortedByCoord.out.dedup.mertrics CREATE_INDEX=true VALIDATION_STRINGENCY=LENIENT AS=true REMOVE_DUPLICATES=true
module load devel;  module load java/1.8.0_131; java -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=primary_keratinocyte-d10.PAS-seq.b2/STAR-2.5.3aAligned.sortedByCoord.out.bam OUTPUT=primary_keratinocyte-d10.PAS-seq.b2/STAR-2.5.3aAligned.sortedByCoord.out.dedup.bam METRICS_FILE=primary_keratinocyte-d10.PAS-seq.b2/STAR-2.5.3aAligned.sortedByCoord.out.dedup.mertrics CREATE_INDEX=true VALIDATION_STRINGENCY=LENIENT AS=true REMOVE_DUPLICATES=true
module load devel;  module load java/1.8.0_131; java -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=primary_keratinocyte-d15.PAS-seq.b1/STAR-2.5.3aAligned.sortedByCoord.out.bam OUTPUT=primary_keratinocyte-d15.PAS-seq.b1/STAR-2.5.3aAligned.sortedByCoord.out.dedup.bam METRICS_FILE=primary_keratinocyte-d15.PAS-seq.b1/STAR-2.5.3aAligned.sortedByCoord.out.dedup.mertrics CREATE_INDEX=true VALIDATION_STRINGENCY=LENIENT AS=true REMOVE_DUPLICATES=true
module load devel;  module load java/1.8.0_131; java -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=primary_keratinocyte-d15.PAS-seq.b2/STAR-2.5.3aAligned.sortedByCoord.out.bam OUTPUT=primary_keratinocyte-d15.PAS-seq.b2/STAR-2.5.3aAligned.sortedByCoord.out.dedup.bam METRICS_FILE=primary_keratinocyte-d15.PAS-seq.b2/STAR-2.5.3aAligned.sortedByCoord.out.dedup.mertrics CREATE_INDEX=true VALIDATION_STRINGENCY=LENIENT AS=true REMOVE_DUPLICATES=true
module load devel;  module load java/1.8.0_131; java -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=primary_keratinocyte-d20.PAS-seq.b1/STAR-2.5.3aAligned.sortedByCoord.out.bam OUTPUT=primary_keratinocyte-d20.PAS-seq.b1/STAR-2.5.3aAligned.sortedByCoord.out.dedup.bam METRICS_FILE=primary_keratinocyte-d20.PAS-seq.b1/STAR-2.5.3aAligned.sortedByCoord.out.dedup.mertrics CREATE_INDEX=true VALIDATION_STRINGENCY=LENIENT AS=true REMOVE_DUPLICATES=true
module load devel;  module load java/1.8.0_131; java -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=primary_keratinocyte-d20.PAS-seq.b2/STAR-2.5.3aAligned.sortedByCoord.out.bam OUTPUT=primary_keratinocyte-d20.PAS-seq.b2/STAR-2.5.3aAligned.sortedByCoord.out.dedup.bam METRICS_FILE=primary_keratinocyte-d20.PAS-seq.b2/STAR-2.5.3aAligned.sortedByCoord.out.dedup.mertrics CREATE_INDEX=true VALIDATION_STRINGENCY=LENIENT AS=true REMOVE_DUPLICATES=true
module load devel;  module load java/1.8.0_131; java -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=primary_keratinocyte-d25.PAS-seq.b1/STAR-2.5.3aAligned.sortedByCoord.out.bam OUTPUT=primary_keratinocyte-d25.PAS-seq.b1/STAR-2.5.3aAligned.sortedByCoord.out.dedup.bam METRICS_FILE=primary_keratinocyte-d25.PAS-seq.b1/STAR-2.5.3aAligned.sortedByCoord.out.dedup.mertrics CREATE_INDEX=true VALIDATION_STRINGENCY=LENIENT AS=true REMOVE_DUPLICATES=true
module load devel;  module load java/1.8.0_131; java -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=primary_keratinocyte-d25.PAS-seq.b2/STAR-2.5.3aAligned.sortedByCoord.out.bam OUTPUT=primary_keratinocyte-d25.PAS-seq.b2/STAR-2.5.3aAligned.sortedByCoord.out.dedup.bam METRICS_FILE=primary_keratinocyte-d25.PAS-seq.b2/STAR-2.5.3aAligned.sortedByCoord.out.dedup.mertrics CREATE_INDEX=true VALIDATION_STRINGENCY=LENIENT AS=true REMOVE_DUPLICATES=true
module load devel;  module load java/1.8.0_131; java -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=primary_keratinocyte-d30.PAS-seq.b1/STAR-2.5.3aAligned.sortedByCoord.out.bam OUTPUT=primary_keratinocyte-d30.PAS-seq.b1/STAR-2.5.3aAligned.sortedByCoord.out.dedup.bam METRICS_FILE=primary_keratinocyte-d30.PAS-seq.b1/STAR-2.5.3aAligned.sortedByCoord.out.dedup.mertrics CREATE_INDEX=true VALIDATION_STRINGENCY=LENIENT AS=true REMOVE_DUPLICATES=true
module load devel;  module load java/1.8.0_131; java -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=primary_keratinocyte-d30.PAS-seq.b2/STAR-2.5.3aAligned.sortedByCoord.out.bam OUTPUT=primary_keratinocyte-d30.PAS-seq.b2/STAR-2.5.3aAligned.sortedByCoord.out.dedup.bam METRICS_FILE=primary_keratinocyte-d30.PAS-seq.b2/STAR-2.5.3aAligned.sortedByCoord.out.dedup.mertrics CREATE_INDEX=true VALIDATION_STRINGENCY=LENIENT AS=true REMOVE_DUPLICATES=true
module load devel;  module load java/1.8.0_131; java -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=primary_keratinocyte-d35.PAS-seq.b1/STAR-2.5.3aAligned.sortedByCoord.out.bam OUTPUT=primary_keratinocyte-d35.PAS-seq.b1/STAR-2.5.3aAligned.sortedByCoord.out.dedup.bam METRICS_FILE=primary_keratinocyte-d35.PAS-seq.b1/STAR-2.5.3aAligned.sortedByCoord.out.dedup.mertrics CREATE_INDEX=true VALIDATION_STRINGENCY=LENIENT AS=true REMOVE_DUPLICATES=true
module load devel;  module load java/1.8.0_131; java -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=primary_keratinocyte-d35.PAS-seq.b2/STAR-2.5.3aAligned.sortedByCoord.out.bam OUTPUT=primary_keratinocyte-d35.PAS-seq.b2/STAR-2.5.3aAligned.sortedByCoord.out.dedup.bam METRICS_FILE=primary_keratinocyte-d35.PAS-seq.b2/STAR-2.5.3aAligned.sortedByCoord.out.dedup.mertrics CREATE_INDEX=true VALIDATION_STRINGENCY=LENIENT AS=true REMOVE_DUPLICATES=true
module load devel;  module load java/1.8.0_131; java -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=primary_keratinocyte-d40.PAS-seq.b1/STAR-2.5.3aAligned.sortedByCoord.out.bam OUTPUT=primary_keratinocyte-d40.PAS-seq.b1/STAR-2.5.3aAligned.sortedByCoord.out.dedup.bam METRICS_FILE=primary_keratinocyte-d40.PAS-seq.b1/STAR-2.5.3aAligned.sortedByCoord.out.dedup.mertrics CREATE_INDEX=true VALIDATION_STRINGENCY=LENIENT AS=true REMOVE_DUPLICATES=true
module load devel;  module load java/1.8.0_131; java -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=primary_keratinocyte-d40.PAS-seq.b2/STAR-2.5.3aAligned.sortedByCoord.out.bam OUTPUT=primary_keratinocyte-d40.PAS-seq.b2/STAR-2.5.3aAligned.sortedByCoord.out.dedup.bam METRICS_FILE=primary_keratinocyte-d40.PAS-seq.b2/STAR-2.5.3aAligned.sortedByCoord.out.dedup.mertrics CREATE_INDEX=true VALIDATION_STRINGENCY=LENIENT AS=true REMOVE_DUPLICATES=true
module load devel;  module load java/1.8.0_131; java -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=primary_keratinocyte-d45.PAS-seq.b1/STAR-2.5.3aAligned.sortedByCoord.out.bam OUTPUT=primary_keratinocyte-d45.PAS-seq.b1/STAR-2.5.3aAligned.sortedByCoord.out.dedup.bam METRICS_FILE=primary_keratinocyte-d45.PAS-seq.b1/STAR-2.5.3aAligned.sortedByCoord.out.dedup.mertrics CREATE_INDEX=true VALIDATION_STRINGENCY=LENIENT AS=true REMOVE_DUPLICATES=true
module load devel;  module load java/1.8.0_131; java -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=primary_keratinocyte-d45.PAS-seq.b2/STAR-2.5.3aAligned.sortedByCoord.out.bam OUTPUT=primary_keratinocyte-d45.PAS-seq.b2/STAR-2.5.3aAligned.sortedByCoord.out.dedup.bam METRICS_FILE=primary_keratinocyte-d45.PAS-seq.b2/STAR-2.5.3aAligned.sortedByCoord.out.dedup.mertrics CREATE_INDEX=true VALIDATION_STRINGENCY=LENIENT AS=true REMOVE_DUPLICATES=true
module load devel;  module load java/1.8.0_131; java -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=primary_keratinocyte-d50.PAS-seq.b1/STAR-2.5.3aAligned.sortedByCoord.out.bam OUTPUT=primary_keratinocyte-d50.PAS-seq.b1/STAR-2.5.3aAligned.sortedByCoord.out.dedup.bam METRICS_FILE=primary_keratinocyte-d50.PAS-seq.b1/STAR-2.5.3aAligned.sortedByCoord.out.dedup.mertrics CREATE_INDEX=true VALIDATION_STRINGENCY=LENIENT AS=true REMOVE_DUPLICATES=true
module load devel;  module load java/1.8.0_131; java -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=primary_keratinocyte-d50.PAS-seq.b2/STAR-2.5.3aAligned.sortedByCoord.out.bam OUTPUT=primary_keratinocyte-d50.PAS-seq.b2/STAR-2.5.3aAligned.sortedByCoord.out.dedup.bam METRICS_FILE=primary_keratinocyte-d50.PAS-seq.b2/STAR-2.5.3aAligned.sortedByCoord.out.dedup.mertrics CREATE_INDEX=true VALIDATION_STRINGENCY=LENIENT AS=true REMOVE_DUPLICATES=true
module load devel;  module load java/1.8.0_131; java -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=primary_keratinocyte-d55.PAS-seq.b1/STAR-2.5.3aAligned.sortedByCoord.out.bam OUTPUT=primary_keratinocyte-d55.PAS-seq.b1/STAR-2.5.3aAligned.sortedByCoord.out.dedup.bam METRICS_FILE=primary_keratinocyte-d55.PAS-seq.b1/STAR-2.5.3aAligned.sortedByCoord.out.dedup.mertrics CREATE_INDEX=true VALIDATION_STRINGENCY=LENIENT AS=true REMOVE_DUPLICATES=true
module load devel;  module load java/1.8.0_131; java -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=primary_keratinocyte-d55.PAS-seq.b2/STAR-2.5.3aAligned.sortedByCoord.out.bam OUTPUT=primary_keratinocyte-d55.PAS-seq.b2/STAR-2.5.3aAligned.sortedByCoord.out.dedup.bam METRICS_FILE=primary_keratinocyte-d55.PAS-seq.b2/STAR-2.5.3aAligned.sortedByCoord.out.dedup.mertrics CREATE_INDEX=true VALIDATION_STRINGENCY=LENIENT AS=true REMOVE_DUPLICATES=true
module load devel;  module load java/1.8.0_131; java -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=primary_keratinocyte-d60.PAS-seq.b1/STAR-2.5.3aAligned.sortedByCoord.out.bam OUTPUT=primary_keratinocyte-d60.PAS-seq.b1/STAR-2.5.3aAligned.sortedByCoord.out.dedup.bam METRICS_FILE=primary_keratinocyte-d60.PAS-seq.b1/STAR-2.5.3aAligned.sortedByCoord.out.dedup.mertrics CREATE_INDEX=true VALIDATION_STRINGENCY=LENIENT AS=true REMOVE_DUPLICATES=true
module load devel;  module load java/1.8.0_131; java -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=primary_keratinocyte-d60.PAS-seq.b2/STAR-2.5.3aAligned.sortedByCoord.out.bam OUTPUT=primary_keratinocyte-d60.PAS-seq.b2/STAR-2.5.3aAligned.sortedByCoord.out.dedup.bam METRICS_FILE=primary_keratinocyte-d60.PAS-seq.b2/STAR-2.5.3aAligned.sortedByCoord.out.dedup.mertrics CREATE_INDEX=true VALIDATION_STRINGENCY=LENIENT AS=true REMOVE_DUPLICATES=true