java -jar /oak/stanford/groups/akundaje/marinovg/programs/Trimmomatic-0.36/trimmomatic-0.36.jar PE 2025-09-16-MS250827L01-exp250721_RPE1_ChIP_1_DMSO_INPUT.end1.fastq.gz 2025-09-16-MS250827L01-exp250721_RPE1_ChIP_1_DMSO_INPUT.end2.fastq.gz 2025-09-16-MS250827L01-exp250721_RPE1_ChIP_1_DMSO_INPUT.end1.paired.fastq.gz 2025-09-16-MS250827L01-exp250721_RPE1_ChIP_1_DMSO_INPUT.end1.unpaired.fastq.gz 2025-09-16-MS250827L01-exp250721_RPE1_ChIP_1_DMSO_INPUT.end2.paired.fastq.gz 2025-09-16-MS250827L01-exp250721_RPE1_ChIP_1_DMSO_INPUT.end2.unpaired.fastq.gz ILLUMINACLIP:/oak/stanford/groups/akundaje/marinovg/programs/Trimmomatic-0.36/adapters/adapters.fa:2:30:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:36 &
java -jar /oak/stanford/groups/akundaje/marinovg/programs/Trimmomatic-0.36/trimmomatic-0.36.jar PE 2025-09-16-MS250827L02-exp250721_RPE1_ChIP_1_TPL_INPUT.end1.fastq.gz 2025-09-16-MS250827L02-exp250721_RPE1_ChIP_1_TPL_INPUT.end2.fastq.gz 2025-09-16-MS250827L02-exp250721_RPE1_ChIP_1_TPL_INPUT.end1.paired.fastq.gz 2025-09-16-MS250827L02-exp250721_RPE1_ChIP_1_TPL_INPUT.end1.unpaired.fastq.gz 2025-09-16-MS250827L02-exp250721_RPE1_ChIP_1_TPL_INPUT.end2.paired.fastq.gz 2025-09-16-MS250827L02-exp250721_RPE1_ChIP_1_TPL_INPUT.end2.unpaired.fastq.gz ILLUMINACLIP:/oak/stanford/groups/akundaje/marinovg/programs/Trimmomatic-0.36/adapters/adapters.fa:2:30:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:36 &
java -jar /oak/stanford/groups/akundaje/marinovg/programs/Trimmomatic-0.36/trimmomatic-0.36.jar PE 2025-09-16-MS250827L03-exp250721_RPE1_ChIP_2_DMSO_INPUT.end1.fastq.gz 2025-09-16-MS250827L03-exp250721_RPE1_ChIP_2_DMSO_INPUT.end2.fastq.gz 2025-09-16-MS250827L03-exp250721_RPE1_ChIP_2_DMSO_INPUT.end1.paired.fastq.gz 2025-09-16-MS250827L03-exp250721_RPE1_ChIP_2_DMSO_INPUT.end1.unpaired.fastq.gz 2025-09-16-MS250827L03-exp250721_RPE1_ChIP_2_DMSO_INPUT.end2.paired.fastq.gz 2025-09-16-MS250827L03-exp250721_RPE1_ChIP_2_DMSO_INPUT.end2.unpaired.fastq.gz ILLUMINACLIP:/oak/stanford/groups/akundaje/marinovg/programs/Trimmomatic-0.36/adapters/adapters.fa:2:30:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:36 &
java -jar /oak/stanford/groups/akundaje/marinovg/programs/Trimmomatic-0.36/trimmomatic-0.36.jar PE 2025-09-16-MS250827L04-exp250721_RPE1_ChIP_2_TPL_INPUT.end1.fastq.gz 2025-09-16-MS250827L04-exp250721_RPE1_ChIP_2_TPL_INPUT.end2.fastq.gz 2025-09-16-MS250827L04-exp250721_RPE1_ChIP_2_TPL_INPUT.end1.paired.fastq.gz 2025-09-16-MS250827L04-exp250721_RPE1_ChIP_2_TPL_INPUT.end1.unpaired.fastq.gz 2025-09-16-MS250827L04-exp250721_RPE1_ChIP_2_TPL_INPUT.end2.paired.fastq.gz 2025-09-16-MS250827L04-exp250721_RPE1_ChIP_2_TPL_INPUT.end2.unpaired.fastq.gz ILLUMINACLIP:/oak/stanford/groups/akundaje/marinovg/programs/Trimmomatic-0.36/adapters/adapters.fa:2:30:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:36 &
java -jar /oak/stanford/groups/akundaje/marinovg/programs/Trimmomatic-0.36/trimmomatic-0.36.jar PE 2025-09-16-MS250827L05-exp250721_RPE1_ChIP_1_DMSO_ChIP.end1.fastq.gz 2025-09-16-MS250827L05-exp250721_RPE1_ChIP_1_DMSO_ChIP.end2.fastq.gz 2025-09-16-MS250827L05-exp250721_RPE1_ChIP_1_DMSO_ChIP.end1.paired.fastq.gz 2025-09-16-MS250827L05-exp250721_RPE1_ChIP_1_DMSO_ChIP.end1.unpaired.fastq.gz 2025-09-16-MS250827L05-exp250721_RPE1_ChIP_1_DMSO_ChIP.end2.paired.fastq.gz 2025-09-16-MS250827L05-exp250721_RPE1_ChIP_1_DMSO_ChIP.end2.unpaired.fastq.gz ILLUMINACLIP:/oak/stanford/groups/akundaje/marinovg/programs/Trimmomatic-0.36/adapters/adapters.fa:2:30:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:36 &
java -jar /oak/stanford/groups/akundaje/marinovg/programs/Trimmomatic-0.36/trimmomatic-0.36.jar PE 2025-09-16-MS250827L06-exp250721_RPE1_ChIP_1_TPL_ChIP.end1.fastq.gz 2025-09-16-MS250827L06-exp250721_RPE1_ChIP_1_TPL_ChIP.end2.fastq.gz 2025-09-16-MS250827L06-exp250721_RPE1_ChIP_1_TPL_ChIP.end1.paired.fastq.gz 2025-09-16-MS250827L06-exp250721_RPE1_ChIP_1_TPL_ChIP.end1.unpaired.fastq.gz 2025-09-16-MS250827L06-exp250721_RPE1_ChIP_1_TPL_ChIP.end2.paired.fastq.gz 2025-09-16-MS250827L06-exp250721_RPE1_ChIP_1_TPL_ChIP.end2.unpaired.fastq.gz ILLUMINACLIP:/oak/stanford/groups/akundaje/marinovg/programs/Trimmomatic-0.36/adapters/adapters.fa:2:30:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:36 &
java -jar /oak/stanford/groups/akundaje/marinovg/programs/Trimmomatic-0.36/trimmomatic-0.36.jar PE 2025-09-16-MS250827L07-exp250721_RPE1_ChIP_2_DMSO_ChIP.end1.fastq.gz 2025-09-16-MS250827L07-exp250721_RPE1_ChIP_2_DMSO_ChIP.end2.fastq.gz 2025-09-16-MS250827L07-exp250721_RPE1_ChIP_2_DMSO_ChIP.end1.paired.fastq.gz 2025-09-16-MS250827L07-exp250721_RPE1_ChIP_2_DMSO_ChIP.end1.unpaired.fastq.gz 2025-09-16-MS250827L07-exp250721_RPE1_ChIP_2_DMSO_ChIP.end2.paired.fastq.gz 2025-09-16-MS250827L07-exp250721_RPE1_ChIP_2_DMSO_ChIP.end2.unpaired.fastq.gz ILLUMINACLIP:/oak/stanford/groups/akundaje/marinovg/programs/Trimmomatic-0.36/adapters/adapters.fa:2:30:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:36 &
java -jar /oak/stanford/groups/akundaje/marinovg/programs/Trimmomatic-0.36/trimmomatic-0.36.jar PE 2025-09-16-MS250827L08-exp250721_RPE1_ChIP_2_TPL_ChIP.end1.fastq.gz 2025-09-16-MS250827L08-exp250721_RPE1_ChIP_2_TPL_ChIP.end2.fastq.gz 2025-09-16-MS250827L08-exp250721_RPE1_ChIP_2_TPL_ChIP.end1.paired.fastq.gz 2025-09-16-MS250827L08-exp250721_RPE1_ChIP_2_TPL_ChIP.end1.unpaired.fastq.gz 2025-09-16-MS250827L08-exp250721_RPE1_ChIP_2_TPL_ChIP.end2.paired.fastq.gz 2025-09-16-MS250827L08-exp250721_RPE1_ChIP_2_TPL_ChIP.end2.unpaired.fastq.gz ILLUMINACLIP:/oak/stanford/groups/akundaje/marinovg/programs/Trimmomatic-0.36/adapters/adapters.fa:2:30:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:36 &
java -jar /oak/stanford/groups/akundaje/marinovg/programs/Trimmomatic-0.36/trimmomatic-0.36.jar PE 2025-09-16-MS250827L09-exp250721_RPE1_ChIP_1_DMSO_Beads.end1.fastq.gz 2025-09-16-MS250827L09-exp250721_RPE1_ChIP_1_DMSO_Beads.end2.fastq.gz 2025-09-16-MS250827L09-exp250721_RPE1_ChIP_1_DMSO_Beads.end1.paired.fastq.gz 2025-09-16-MS250827L09-exp250721_RPE1_ChIP_1_DMSO_Beads.end1.unpaired.fastq.gz 2025-09-16-MS250827L09-exp250721_RPE1_ChIP_1_DMSO_Beads.end2.paired.fastq.gz 2025-09-16-MS250827L09-exp250721_RPE1_ChIP_1_DMSO_Beads.end2.unpaired.fastq.gz ILLUMINACLIP:/oak/stanford/groups/akundaje/marinovg/programs/Trimmomatic-0.36/adapters/adapters.fa:2:30:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:36 &
java -jar /oak/stanford/groups/akundaje/marinovg/programs/Trimmomatic-0.36/trimmomatic-0.36.jar PE 2025-09-16-MS250827L10-exp250721_RPE1_ChIP_1_TPL_Beads.end1.fastq.gz 2025-09-16-MS250827L10-exp250721_RPE1_ChIP_1_TPL_Beads.end2.fastq.gz 2025-09-16-MS250827L10-exp250721_RPE1_ChIP_1_TPL_Beads.end1.paired.fastq.gz 2025-09-16-MS250827L10-exp250721_RPE1_ChIP_1_TPL_Beads.end1.unpaired.fastq.gz 2025-09-16-MS250827L10-exp250721_RPE1_ChIP_1_TPL_Beads.end2.paired.fastq.gz 2025-09-16-MS250827L10-exp250721_RPE1_ChIP_1_TPL_Beads.end2.unpaired.fastq.gz ILLUMINACLIP:/oak/stanford/groups/akundaje/marinovg/programs/Trimmomatic-0.36/adapters/adapters.fa:2:30:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:36 &
java -jar /oak/stanford/groups/akundaje/marinovg/programs/Trimmomatic-0.36/trimmomatic-0.36.jar PE 2025-09-16-MS250827L11-exp250721_RPE1_ChIP_2_DMSO_Beads.end1.fastq.gz 2025-09-16-MS250827L11-exp250721_RPE1_ChIP_2_DMSO_Beads.end2.fastq.gz 2025-09-16-MS250827L11-exp250721_RPE1_ChIP_2_DMSO_Beads.end1.paired.fastq.gz 2025-09-16-MS250827L11-exp250721_RPE1_ChIP_2_DMSO_Beads.end1.unpaired.fastq.gz 2025-09-16-MS250827L11-exp250721_RPE1_ChIP_2_DMSO_Beads.end2.paired.fastq.gz 2025-09-16-MS250827L11-exp250721_RPE1_ChIP_2_DMSO_Beads.end2.unpaired.fastq.gz ILLUMINACLIP:/oak/stanford/groups/akundaje/marinovg/programs/Trimmomatic-0.36/adapters/adapters.fa:2:30:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:36 &
java -jar /oak/stanford/groups/akundaje/marinovg/programs/Trimmomatic-0.36/trimmomatic-0.36.jar PE 2025-09-16-MS250827L12-exp250721_RPE1_ChIP_2_TPL_Beads.end1.fastq.gz 2025-09-16-MS250827L12-exp250721_RPE1_ChIP_2_TPL_Beads.end2.fastq.gz 2025-09-16-MS250827L12-exp250721_RPE1_ChIP_2_TPL_Beads.end1.paired.fastq.gz 2025-09-16-MS250827L12-exp250721_RPE1_ChIP_2_TPL_Beads.end1.unpaired.fastq.gz 2025-09-16-MS250827L12-exp250721_RPE1_ChIP_2_TPL_Beads.end2.paired.fastq.gz 2025-09-16-MS250827L12-exp250721_RPE1_ChIP_2_TPL_Beads.end2.unpaired.fastq.gz ILLUMINACLIP:/oak/stanford/groups/akundaje/marinovg/programs/Trimmomatic-0.36/adapters/adapters.fa:2:30:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:36 &
java -jar /oak/stanford/groups/akundaje/marinovg/programs/Trimmomatic-0.36/trimmomatic-0.36.jar PE 2025-09-16-MS250902L13-exp250728_RPE1_ChIP_Palbo-18h_INPUT.end1.fastq.gz 2025-09-16-MS250902L13-exp250728_RPE1_ChIP_Palbo-18h_INPUT.end2.fastq.gz 2025-09-16-MS250902L13-exp250728_RPE1_ChIP_Palbo-18h_INPUT.end1.paired.fastq.gz 2025-09-16-MS250902L13-exp250728_RPE1_ChIP_Palbo-18h_INPUT.end1.unpaired.fastq.gz 2025-09-16-MS250902L13-exp250728_RPE1_ChIP_Palbo-18h_INPUT.end2.paired.fastq.gz 2025-09-16-MS250902L13-exp250728_RPE1_ChIP_Palbo-18h_INPUT.end2.unpaired.fastq.gz ILLUMINACLIP:/oak/stanford/groups/akundaje/marinovg/programs/Trimmomatic-0.36/adapters/adapters.fa:2:30:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:36 &
java -jar /oak/stanford/groups/akundaje/marinovg/programs/Trimmomatic-0.36/trimmomatic-0.36.jar PE 2025-09-16-MS250902L14-exp250728_RPE1_ChIP_Palbo-48h_INPUT.end1.fastq.gz 2025-09-16-MS250902L14-exp250728_RPE1_ChIP_Palbo-48h_INPUT.end2.fastq.gz 2025-09-16-MS250902L14-exp250728_RPE1_ChIP_Palbo-48h_INPUT.end1.paired.fastq.gz 2025-09-16-MS250902L14-exp250728_RPE1_ChIP_Palbo-48h_INPUT.end1.unpaired.fastq.gz 2025-09-16-MS250902L14-exp250728_RPE1_ChIP_Palbo-48h_INPUT.end2.paired.fastq.gz 2025-09-16-MS250902L14-exp250728_RPE1_ChIP_Palbo-48h_INPUT.end2.unpaired.fastq.gz ILLUMINACLIP:/oak/stanford/groups/akundaje/marinovg/programs/Trimmomatic-0.36/adapters/adapters.fa:2:30:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:36 &
java -jar /oak/stanford/groups/akundaje/marinovg/programs/Trimmomatic-0.36/trimmomatic-0.36.jar PE 2025-09-16-MS250902L15-exp250728_RPE1_ChIP_Palbo-96h_INPUT.end1.fastq.gz 2025-09-16-MS250902L15-exp250728_RPE1_ChIP_Palbo-96h_INPUT.end2.fastq.gz 2025-09-16-MS250902L15-exp250728_RPE1_ChIP_Palbo-96h_INPUT.end1.paired.fastq.gz 2025-09-16-MS250902L15-exp250728_RPE1_ChIP_Palbo-96h_INPUT.end1.unpaired.fastq.gz 2025-09-16-MS250902L15-exp250728_RPE1_ChIP_Palbo-96h_INPUT.end2.paired.fastq.gz 2025-09-16-MS250902L15-exp250728_RPE1_ChIP_Palbo-96h_INPUT.end2.unpaired.fastq.gz ILLUMINACLIP:/oak/stanford/groups/akundaje/marinovg/programs/Trimmomatic-0.36/adapters/adapters.fa:2:30:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:36 &
java -jar /oak/stanford/groups/akundaje/marinovg/programs/Trimmomatic-0.36/trimmomatic-0.36.jar PE 2025-09-16-MS250902L16-exp250728_RPE1_ChIP_Palbo-18h_ChIP.end1.fastq.gz 2025-09-16-MS250902L16-exp250728_RPE1_ChIP_Palbo-18h_ChIP.end2.fastq.gz 2025-09-16-MS250902L16-exp250728_RPE1_ChIP_Palbo-18h_ChIP.end1.paired.fastq.gz 2025-09-16-MS250902L16-exp250728_RPE1_ChIP_Palbo-18h_ChIP.end1.unpaired.fastq.gz 2025-09-16-MS250902L16-exp250728_RPE1_ChIP_Palbo-18h_ChIP.end2.paired.fastq.gz 2025-09-16-MS250902L16-exp250728_RPE1_ChIP_Palbo-18h_ChIP.end2.unpaired.fastq.gz ILLUMINACLIP:/oak/stanford/groups/akundaje/marinovg/programs/Trimmomatic-0.36/adapters/adapters.fa:2:30:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:36 &
java -jar /oak/stanford/groups/akundaje/marinovg/programs/Trimmomatic-0.36/trimmomatic-0.36.jar PE 2025-09-16-MS250902L17-exp250728_RPE1_ChIP_Palbo-48h_ChIP.end1.fastq.gz 2025-09-16-MS250902L17-exp250728_RPE1_ChIP_Palbo-48h_ChIP.end2.fastq.gz 2025-09-16-MS250902L17-exp250728_RPE1_ChIP_Palbo-48h_ChIP.end1.paired.fastq.gz 2025-09-16-MS250902L17-exp250728_RPE1_ChIP_Palbo-48h_ChIP.end1.unpaired.fastq.gz 2025-09-16-MS250902L17-exp250728_RPE1_ChIP_Palbo-48h_ChIP.end2.paired.fastq.gz 2025-09-16-MS250902L17-exp250728_RPE1_ChIP_Palbo-48h_ChIP.end2.unpaired.fastq.gz ILLUMINACLIP:/oak/stanford/groups/akundaje/marinovg/programs/Trimmomatic-0.36/adapters/adapters.fa:2:30:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:36 &
java -jar /oak/stanford/groups/akundaje/marinovg/programs/Trimmomatic-0.36/trimmomatic-0.36.jar PE 2025-09-16-MS250902L18-exp250728_RPE1_ChIP_Palbo-96h_ChIP.end1.fastq.gz 2025-09-16-MS250902L18-exp250728_RPE1_ChIP_Palbo-96h_ChIP.end2.fastq.gz 2025-09-16-MS250902L18-exp250728_RPE1_ChIP_Palbo-96h_ChIP.end1.paired.fastq.gz 2025-09-16-MS250902L18-exp250728_RPE1_ChIP_Palbo-96h_ChIP.end1.unpaired.fastq.gz 2025-09-16-MS250902L18-exp250728_RPE1_ChIP_Palbo-96h_ChIP.end2.paired.fastq.gz 2025-09-16-MS250902L18-exp250728_RPE1_ChIP_Palbo-96h_ChIP.end2.unpaired.fastq.gz ILLUMINACLIP:/oak/stanford/groups/akundaje/marinovg/programs/Trimmomatic-0.36/adapters/adapters.fa:2:30:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:36 &