java -jar /oak/stanford/groups/akundaje/marinovg/programs/Trimmomatic-0.36/trimmomatic-0.36.jar PE DB115_Br2-CRR994956_f1.fastq.gz DB115_Br2-CRR994956_r2.fastq.gz DB115_Br2-CRR994956.read1.paired.fastq.gz DB115_Br2-CRR994956.read1.unpaired.fastq.gz DB115_Br2-CRR994956.read2.paired.fastq.gz DB115_Br2-CRR994956.read2.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 DB115_Br3-CRR994957_f1.fastq.gz DB115_Br3-CRR994957_r2.fastq.gz DB115_Br3-CRR994957.read1.paired.fastq.gz DB115_Br3-CRR994957.read1.unpaired.fastq.gz DB115_Br3-CRR994957.read2.paired.fastq.gz DB115_Br3-CRR994957.read2.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 DB115_Li2-CRR994959_f1.fastq.gz DB115_Li2-CRR994959_r2.fastq.gz DB115_Li2-CRR994959.read1.paired.fastq.gz DB115_Li2-CRR994959.read1.unpaired.fastq.gz DB115_Li2-CRR994959.read2.paired.fastq.gz DB115_Li2-CRR994959.read2.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 DB115_Li3-CRR994960_f1.fastq.gz DB115_Li3-CRR994960_r2.fastq.gz DB115_Li3-CRR994960.read1.paired.fastq.gz DB115_Li3-CRR994960.read1.unpaired.fastq.gz DB115_Li3-CRR994960.read2.paired.fastq.gz DB115_Li3-CRR994960.read2.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 DB115_Mu1-CRR994961_f1.fastq.gz DB115_Mu1-CRR994961_r2.fastq.gz DB115_Mu1-CRR994961.read1.paired.fastq.gz DB115_Mu1-CRR994961.read1.unpaired.fastq.gz DB115_Mu1-CRR994961.read2.paired.fastq.gz DB115_Mu1-CRR994961.read2.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 DB115_Mu2-CRR994962_f1.fastq.gz DB115_Mu2-CRR994962_r2.fastq.gz DB115_Mu2-CRR994962.read1.paired.fastq.gz DB115_Mu2-CRR994962.read1.unpaired.fastq.gz DB115_Mu2-CRR994962.read2.paired.fastq.gz DB115_Mu2-CRR994962.read2.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 DB115_Mu3-CRR994963_f1.fastq.gz DB115_Mu3-CRR994963_r2.fastq.gz DB115_Mu3-CRR994963.read1.paired.fastq.gz DB115_Mu3-CRR994963.read1.unpaired.fastq.gz DB115_Mu3-CRR994963.read2.paired.fastq.gz DB115_Mu3-CRR994963.read2.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 DB168_E_Br1-CRR994964_f1.fastq.gz DB168_E_Br1-CRR994964_r2.fastq.gz DB168_E_Br1-CRR994964.read1.paired.fastq.gz DB168_E_Br1-CRR994964.read1.unpaired.fastq.gz DB168_E_Br1-CRR994964.read2.paired.fastq.gz DB168_E_Br1-CRR994964.read2.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 DB168_E_Li1-CRR994965_f1.fastq.gz DB168_E_Li1-CRR994965_r2.fastq.gz DB168_E_Li1-CRR994965.read1.paired.fastq.gz DB168_E_Li1-CRR994965.read1.unpaired.fastq.gz DB168_E_Li1-CRR994965.read2.paired.fastq.gz DB168_E_Li1-CRR994965.read2.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 DB168_I_Br2-CRR994967_f1.fastq.gz DB168_I_Br2-CRR994967_r2.fastq.gz DB168_I_Br2-CRR994967.read1.paired.fastq.gz DB168_I_Br2-CRR994967.read1.unpaired.fastq.gz DB168_I_Br2-CRR994967.read2.paired.fastq.gz DB168_I_Br2-CRR994967.read2.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 DB168_I_Li2-CRR994968_f1.fastq.gz DB168_I_Li2-CRR994968_r2.fastq.gz DB168_I_Li2-CRR994968.read1.paired.fastq.gz DB168_I_Li2-CRR994968.read1.unpaired.fastq.gz DB168_I_Li2-CRR994968.read2.paired.fastq.gz DB168_I_Li2-CRR994968.read2.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 DB168_I_Mu2-CRR994969_f1.fastq.gz DB168_I_Mu2-CRR994969_r2.fastq.gz DB168_I_Mu2-CRR994969.read1.paired.fastq.gz DB168_I_Mu2-CRR994969.read1.unpaired.fastq.gz DB168_I_Mu2-CRR994969.read2.paired.fastq.gz DB168_I_Mu2-CRR994969.read2.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 DB168_J_Br3-CRR994970_f1.fastq.gz DB168_J_Br3-CRR994970_r2.fastq.gz DB168_J_Br3-CRR994970.read1.paired.fastq.gz DB168_J_Br3-CRR994970.read1.unpaired.fastq.gz DB168_J_Br3-CRR994970.read2.paired.fastq.gz DB168_J_Br3-CRR994970.read2.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 DB168_J_Li3-CRR994971_f1.fastq.gz DB168_J_Li3-CRR994971_r2.fastq.gz DB168_J_Li3-CRR994971.read1.paired.fastq.gz DB168_J_Li3-CRR994971.read1.unpaired.fastq.gz DB168_J_Li3-CRR994971.read2.paired.fastq.gz DB168_J_Li3-CRR994971.read2.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 DB168_J_Mu3-CRR994972_f1.fastq.gz DB168_J_Mu3-CRR994972_r2.fastq.gz DB168_J_Mu3-CRR994972.read1.paired.fastq.gz DB168_J_Mu3-CRR994972.read1.unpaired.fastq.gz DB168_J_Mu3-CRR994972.read2.paired.fastq.gz DB168_J_Mu3-CRR994972.read2.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 DB40_Br1-CRR994973_f1.fastq.gz DB40_Br1-CRR994973_r2.fastq.gz DB40_Br1-CRR994973.read1.paired.fastq.gz DB40_Br1-CRR994973.read1.unpaired.fastq.gz DB40_Br1-CRR994973.read2.paired.fastq.gz DB40_Br1-CRR994973.read2.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 DB40_Li1-CRR994976_f1.fastq.gz DB40_Li1-CRR994976_r2.fastq.gz DB40_Li1-CRR994976.read1.paired.fastq.gz DB40_Li1-CRR994976.read1.unpaired.fastq.gz DB40_Li1-CRR994976.read2.paired.fastq.gz DB40_Li1-CRR994976.read2.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 DB40_Li2-CRR994977_f1.fastq.gz DB40_Li2-CRR994977_r2.fastq.gz DB40_Li2-CRR994977.read1.paired.fastq.gz DB40_Li2-CRR994977.read1.unpaired.fastq.gz DB40_Li2-CRR994977.read2.paired.fastq.gz DB40_Li2-CRR994977.read2.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 DB40_Li3-CRR994978_f1.fastq.gz DB40_Li3-CRR994978_r2.fastq.gz DB40_Li3-CRR994978.read1.paired.fastq.gz DB40_Li3-CRR994978.read1.unpaired.fastq.gz DB40_Li3-CRR994978.read2.paired.fastq.gz DB40_Li3-CRR994978.read2.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 DB40_Mu1-CRR994979_f1.fastq.gz DB40_Mu1-CRR994979_r2.fastq.gz DB40_Mu1-CRR994979.read1.paired.fastq.gz DB40_Mu1-CRR994979.read1.unpaired.fastq.gz DB40_Mu1-CRR994979.read2.paired.fastq.gz DB40_Mu1-CRR994979.read2.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 DB40_Mu2-CRR994980_f1.fastq.gz DB40_Mu2-CRR994980_r2.fastq.gz DB40_Mu2-CRR994980.read1.paired.fastq.gz DB40_Mu2-CRR994980.read1.unpaired.fastq.gz DB40_Mu2-CRR994980.read2.paired.fastq.gz DB40_Mu2-CRR994980.read2.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 DB40_Mu3-CRR994981_f1.fastq.gz DB40_Mu3-CRR994981_r2.fastq.gz DB40_Mu3-CRR994981.read1.paired.fastq.gz DB40_Mu3-CRR994981.read1.unpaired.fastq.gz DB40_Mu3-CRR994981.read2.paired.fastq.gz DB40_Mu3-CRR994981.read2.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 DB40_Pl1-CRR994982_f1.fastq.gz DB40_Pl1-CRR994982_r2.fastq.gz DB40_Pl1-CRR994982.read1.paired.fastq.gz DB40_Pl1-CRR994982.read1.unpaired.fastq.gz DB40_Pl1-CRR994982.read2.paired.fastq.gz DB40_Pl1-CRR994982.read2.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 DB40_Pl2-CRR994983_f1.fastq.gz DB40_Pl2-CRR994983_r2.fastq.gz DB40_Pl2-CRR994983.read1.paired.fastq.gz DB40_Pl2-CRR994983.read1.unpaired.fastq.gz DB40_Pl2-CRR994983.read2.paired.fastq.gz DB40_Pl2-CRR994983.read2.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 DB40_Pl3-CRR994984_f1.fastq.gz DB40_Pl3-CRR994984_r2.fastq.gz DB40_Pl3-CRR994984.read1.paired.fastq.gz DB40_Pl3-CRR994984.read1.unpaired.fastq.gz DB40_Pl3-CRR994984.read2.paired.fastq.gz DB40_Pl3-CRR994984.read2.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 DB70_Br1-CRR994985_f1.fastq.gz DB70_Br1-CRR994985_r2.fastq.gz DB70_Br1-CRR994985.read1.paired.fastq.gz DB70_Br1-CRR994985.read1.unpaired.fastq.gz DB70_Br1-CRR994985.read2.paired.fastq.gz DB70_Br1-CRR994985.read2.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 DB70_Br3-CRR994987_f1.fastq.gz DB70_Br3-CRR994987_r2.fastq.gz DB70_Br3-CRR994987.read1.paired.fastq.gz DB70_Br3-CRR994987.read1.unpaired.fastq.gz DB70_Br3-CRR994987.read2.paired.fastq.gz DB70_Br3-CRR994987.read2.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 DB70_Li2-CRR994989_f1.fastq.gz DB70_Li2-CRR994989_r2.fastq.gz DB70_Li2-CRR994989.read1.paired.fastq.gz DB70_Li2-CRR994989.read1.unpaired.fastq.gz DB70_Li2-CRR994989.read2.paired.fastq.gz DB70_Li2-CRR994989.read2.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 DB70_Li3-CRR994990_f1.fastq.gz DB70_Li3-CRR994990_r2.fastq.gz DB70_Li3-CRR994990.read1.paired.fastq.gz DB70_Li3-CRR994990.read1.unpaired.fastq.gz DB70_Li3-CRR994990.read2.paired.fastq.gz DB70_Li3-CRR994990.read2.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 DB70_Mu1-CRR994991_f1.fastq.gz DB70_Mu1-CRR994991_r2.fastq.gz DB70_Mu1-CRR994991.read1.paired.fastq.gz DB70_Mu1-CRR994991.read1.unpaired.fastq.gz DB70_Mu1-CRR994991.read2.paired.fastq.gz DB70_Mu1-CRR994991.read2.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 DB70_Mu2-CRR994992_f1.fastq.gz DB70_Mu2-CRR994992_r2.fastq.gz DB70_Mu2-CRR994992.read1.paired.fastq.gz DB70_Mu2-CRR994992.read1.unpaired.fastq.gz DB70_Mu2-CRR994992.read2.paired.fastq.gz DB70_Mu2-CRR994992.read2.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 DB70_Mu3-CRR994993_f1.fastq.gz DB70_Mu3-CRR994993_r2.fastq.gz DB70_Mu3-CRR994993.read1.paired.fastq.gz DB70_Mu3-CRR994993.read1.unpaired.fastq.gz DB70_Mu3-CRR994993.read2.paired.fastq.gz DB70_Mu3-CRR994993.read2.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 DB70_Pl1-CRR994994_f1.fastq.gz DB70_Pl1-CRR994994_r2.fastq.gz DB70_Pl1-CRR994994.read1.paired.fastq.gz DB70_Pl1-CRR994994.read1.unpaired.fastq.gz DB70_Pl1-CRR994994.read2.paired.fastq.gz DB70_Pl1-CRR994994.read2.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 DS115_Br1-CRR994995_f1.fastq.gz DS115_Br1-CRR994995_r2.fastq.gz DS115_Br1-CRR994995.read1.paired.fastq.gz DS115_Br1-CRR994995.read1.unpaired.fastq.gz DS115_Br1-CRR994995.read2.paired.fastq.gz DS115_Br1-CRR994995.read2.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 DS115_Br2-CRR994996_f1.fastq.gz DS115_Br2-CRR994996_r2.fastq.gz DS115_Br2-CRR994996.read1.paired.fastq.gz DS115_Br2-CRR994996.read1.unpaired.fastq.gz DS115_Br2-CRR994996.read2.paired.fastq.gz DS115_Br2-CRR994996.read2.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 DS115_Br3-CRR994997_f1.fastq.gz DS115_Br3-CRR994997_r2.fastq.gz DS115_Br3-CRR994997.read1.paired.fastq.gz DS115_Br3-CRR994997.read1.unpaired.fastq.gz DS115_Br3-CRR994997.read2.paired.fastq.gz DS115_Br3-CRR994997.read2.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 DS115_Li1-CRR994998_f1.fastq.gz DS115_Li1-CRR994998_r2.fastq.gz DS115_Li1-CRR994998.read1.paired.fastq.gz DS115_Li1-CRR994998.read1.unpaired.fastq.gz DS115_Li1-CRR994998.read2.paired.fastq.gz DS115_Li1-CRR994998.read2.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 DS115_Li2-CRR994999_f1.fastq.gz DS115_Li2-CRR994999_r2.fastq.gz DS115_Li2-CRR994999.read1.paired.fastq.gz DS115_Li2-CRR994999.read1.unpaired.fastq.gz DS115_Li2-CRR994999.read2.paired.fastq.gz DS115_Li2-CRR994999.read2.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 DS115_Li3-CRR995000_f1.fastq.gz DS115_Li3-CRR995000_r2.fastq.gz DS115_Li3-CRR995000.read1.paired.fastq.gz DS115_Li3-CRR995000.read1.unpaired.fastq.gz DS115_Li3-CRR995000.read2.paired.fastq.gz DS115_Li3-CRR995000.read2.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 DS115_Mu1-CRR995001_f1.fastq.gz DS115_Mu1-CRR995001_r2.fastq.gz DS115_Mu1-CRR995001.read1.paired.fastq.gz DS115_Mu1-CRR995001.read1.unpaired.fastq.gz DS115_Mu1-CRR995001.read2.paired.fastq.gz DS115_Mu1-CRR995001.read2.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 DS115_Mu2-CRR995002_f1.fastq.gz DS115_Mu2-CRR995002_r2.fastq.gz DS115_Mu2-CRR995002.read1.paired.fastq.gz DS115_Mu2-CRR995002.read1.unpaired.fastq.gz DS115_Mu2-CRR995002.read2.paired.fastq.gz DS115_Mu2-CRR995002.read2.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 DS115_Mu3-CRR995003_f1.fastq.gz DS115_Mu3-CRR995003_r2.fastq.gz DS115_Mu3-CRR995003.read1.paired.fastq.gz DS115_Mu3-CRR995003.read1.unpaired.fastq.gz DS115_Mu3-CRR995003.read2.paired.fastq.gz DS115_Mu3-CRR995003.read2.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 DS168_M_Br1-CRR995004_f1.fastq.gz DS168_M_Br1-CRR995004_r2.fastq.gz DS168_M_Br1-CRR995004.read1.paired.fastq.gz DS168_M_Br1-CRR995004.read1.unpaired.fastq.gz DS168_M_Br1-CRR995004.read2.paired.fastq.gz DS168_M_Br1-CRR995004.read2.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 DS168_M_Li1-CRR995005_f1.fastq.gz DS168_M_Li1-CRR995005_r2.fastq.gz DS168_M_Li1-CRR995005.read1.paired.fastq.gz DS168_M_Li1-CRR995005.read1.unpaired.fastq.gz DS168_M_Li1-CRR995005.read2.paired.fastq.gz DS168_M_Li1-CRR995005.read2.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 DS168_N_Br2-CRR995007_f1.fastq.gz DS168_N_Br2-CRR995007_r2.fastq.gz DS168_N_Br2-CRR995007.read1.paired.fastq.gz DS168_N_Br2-CRR995007.read1.unpaired.fastq.gz DS168_N_Br2-CRR995007.read2.paired.fastq.gz DS168_N_Br2-CRR995007.read2.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 DS168_N_Li2-CRR995008_f1.fastq.gz DS168_N_Li2-CRR995008_r2.fastq.gz DS168_N_Li2-CRR995008.read1.paired.fastq.gz DS168_N_Li2-CRR995008.read1.unpaired.fastq.gz DS168_N_Li2-CRR995008.read2.paired.fastq.gz DS168_N_Li2-CRR995008.read2.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 DS168_N_Mu2-CRR995009_f1.fastq.gz DS168_N_Mu2-CRR995009_r2.fastq.gz DS168_N_Mu2-CRR995009.read1.paired.fastq.gz DS168_N_Mu2-CRR995009.read1.unpaired.fastq.gz DS168_N_Mu2-CRR995009.read2.paired.fastq.gz DS168_N_Mu2-CRR995009.read2.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 DS168_O_Br3-CRR995010_f1.fastq.gz DS168_O_Br3-CRR995010_r2.fastq.gz DS168_O_Br3-CRR995010.read1.paired.fastq.gz DS168_O_Br3-CRR995010.read1.unpaired.fastq.gz DS168_O_Br3-CRR995010.read2.paired.fastq.gz DS168_O_Br3-CRR995010.read2.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 DS168_O_Li3-CRR995011_f1.fastq.gz DS168_O_Li3-CRR995011_r2.fastq.gz DS168_O_Li3-CRR995011.read1.paired.fastq.gz DS168_O_Li3-CRR995011.read1.unpaired.fastq.gz DS168_O_Li3-CRR995011.read2.paired.fastq.gz DS168_O_Li3-CRR995011.read2.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 DS40_Br1-CRR995013_f1.fastq.gz DS40_Br1-CRR995013_r2.fastq.gz DS40_Br1-CRR995013.read1.paired.fastq.gz DS40_Br1-CRR995013.read1.unpaired.fastq.gz DS40_Br1-CRR995013.read2.paired.fastq.gz DS40_Br1-CRR995013.read2.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 DS40_Br2-CRR995014_f1.fastq.gz DS40_Br2-CRR995014_r2.fastq.gz DS40_Br2-CRR995014.read1.paired.fastq.gz DS40_Br2-CRR995014.read1.unpaired.fastq.gz DS40_Br2-CRR995014.read2.paired.fastq.gz DS40_Br2-CRR995014.read2.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 DS40_Br3-CRR995015_f1.fastq.gz DS40_Br3-CRR995015_r2.fastq.gz DS40_Br3-CRR995015.read1.paired.fastq.gz DS40_Br3-CRR995015.read1.unpaired.fastq.gz DS40_Br3-CRR995015.read2.paired.fastq.gz DS40_Br3-CRR995015.read2.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 DS40_Li2-CRR995016_f1.fastq.gz DS40_Li2-CRR995016_r2.fastq.gz DS40_Li2-CRR995016.read1.paired.fastq.gz DS40_Li2-CRR995016.read1.unpaired.fastq.gz DS40_Li2-CRR995016.read2.paired.fastq.gz DS40_Li2-CRR995016.read2.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 DS40_Li3-CRR995017_f1.fastq.gz DS40_Li3-CRR995017_r2.fastq.gz DS40_Li3-CRR995017.read1.paired.fastq.gz DS40_Li3-CRR995017.read1.unpaired.fastq.gz DS40_Li3-CRR995017.read2.paired.fastq.gz DS40_Li3-CRR995017.read2.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 DS40_Mu1-CRR995018_f1.fastq.gz DS40_Mu1-CRR995018_r2.fastq.gz DS40_Mu1-CRR995018.read1.paired.fastq.gz DS40_Mu1-CRR995018.read1.unpaired.fastq.gz DS40_Mu1-CRR995018.read2.paired.fastq.gz DS40_Mu1-CRR995018.read2.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 DS40_Mu2-CRR995019_f1.fastq.gz DS40_Mu2-CRR995019_r2.fastq.gz DS40_Mu2-CRR995019.read1.paired.fastq.gz DS40_Mu2-CRR995019.read1.unpaired.fastq.gz DS40_Mu2-CRR995019.read2.paired.fastq.gz DS40_Mu2-CRR995019.read2.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 DS40_Mu3-CRR995020_f1.fastq.gz DS40_Mu3-CRR995020_r2.fastq.gz DS40_Mu3-CRR995020.read1.paired.fastq.gz DS40_Mu3-CRR995020.read1.unpaired.fastq.gz DS40_Mu3-CRR995020.read2.paired.fastq.gz DS40_Mu3-CRR995020.read2.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 DS40_Pl1-CRR995021_f1.fastq.gz DS40_Pl1-CRR995021_r2.fastq.gz DS40_Pl1-CRR995021.read1.paired.fastq.gz DS40_Pl1-CRR995021.read1.unpaired.fastq.gz DS40_Pl1-CRR995021.read2.paired.fastq.gz DS40_Pl1-CRR995021.read2.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 DS40_Pl2-CRR995022_f1.fastq.gz DS40_Pl2-CRR995022_r2.fastq.gz DS40_Pl2-CRR995022.read1.paired.fastq.gz DS40_Pl2-CRR995022.read1.unpaired.fastq.gz DS40_Pl2-CRR995022.read2.paired.fastq.gz DS40_Pl2-CRR995022.read2.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 DS40_Pl3-CRR995023_f1.fastq.gz DS40_Pl3-CRR995023_r2.fastq.gz DS40_Pl3-CRR995023.read1.paired.fastq.gz DS40_Pl3-CRR995023.read1.unpaired.fastq.gz DS40_Pl3-CRR995023.read2.paired.fastq.gz DS40_Pl3-CRR995023.read2.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 DS70_Br1-CRR995024_f1.fastq.gz DS70_Br1-CRR995024_r2.fastq.gz DS70_Br1-CRR995024.read1.paired.fastq.gz DS70_Br1-CRR995024.read1.unpaired.fastq.gz DS70_Br1-CRR995024.read2.paired.fastq.gz DS70_Br1-CRR995024.read2.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 DS70_Br2-CRR995025_f1.fastq.gz DS70_Br2-CRR995025_r2.fastq.gz DS70_Br2-CRR995025.read1.paired.fastq.gz DS70_Br2-CRR995025.read1.unpaired.fastq.gz DS70_Br2-CRR995025.read2.paired.fastq.gz DS70_Br2-CRR995025.read2.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 DS70_Br3-CRR995026_f1.fastq.gz DS70_Br3-CRR995026_r2.fastq.gz DS70_Br3-CRR995026.read1.paired.fastq.gz DS70_Br3-CRR995026.read1.unpaired.fastq.gz DS70_Br3-CRR995026.read2.paired.fastq.gz DS70_Br3-CRR995026.read2.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 DS70_Li1-CRR995027_f1.fastq.gz DS70_Li1-CRR995027_r2.fastq.gz DS70_Li1-CRR995027.read1.paired.fastq.gz DS70_Li1-CRR995027.read1.unpaired.fastq.gz DS70_Li1-CRR995027.read2.paired.fastq.gz DS70_Li1-CRR995027.read2.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 DS70_Li2-CRR995028_f1.fastq.gz DS70_Li2-CRR995028_r2.fastq.gz DS70_Li2-CRR995028.read1.paired.fastq.gz DS70_Li2-CRR995028.read1.unpaired.fastq.gz DS70_Li2-CRR995028.read2.paired.fastq.gz DS70_Li2-CRR995028.read2.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 DS70_Li3-CRR995029_f1.fastq.gz DS70_Li3-CRR995029_r2.fastq.gz DS70_Li3-CRR995029.read1.paired.fastq.gz DS70_Li3-CRR995029.read1.unpaired.fastq.gz DS70_Li3-CRR995029.read2.paired.fastq.gz DS70_Li3-CRR995029.read2.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 DS70_Mu1-CRR995030_f1.fastq.gz DS70_Mu1-CRR995030_r2.fastq.gz DS70_Mu1-CRR995030.read1.paired.fastq.gz DS70_Mu1-CRR995030.read1.unpaired.fastq.gz DS70_Mu1-CRR995030.read2.paired.fastq.gz DS70_Mu1-CRR995030.read2.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 DS70_Mu2-CRR995031_f1.fastq.gz DS70_Mu2-CRR995031_r2.fastq.gz DS70_Mu2-CRR995031.read1.paired.fastq.gz DS70_Mu2-CRR995031.read1.unpaired.fastq.gz DS70_Mu2-CRR995031.read2.paired.fastq.gz DS70_Mu2-CRR995031.read2.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 DS70_Mu3-CRR995032_f1.fastq.gz DS70_Mu3-CRR995032_r2.fastq.gz DS70_Mu3-CRR995032.read1.paired.fastq.gz DS70_Mu3-CRR995032.read1.unpaired.fastq.gz DS70_Mu3-CRR995032.read2.paired.fastq.gz DS70_Mu3-CRR995032.read2.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 DS70_Pl1-CRR995033_f1.fastq.gz DS70_Pl1-CRR995033_r2.fastq.gz DS70_Pl1-CRR995033.read1.paired.fastq.gz DS70_Pl1-CRR995033.read1.unpaired.fastq.gz DS70_Pl1-CRR995033.read2.paired.fastq.gz DS70_Pl1-CRR995033.read2.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 DS70_Pl3-CRR995034_f1.fastq.gz DS70_Pl3-CRR995034_r2.fastq.gz DS70_Pl3-CRR995034.read1.paired.fastq.gz DS70_Pl3-CRR995034.read1.unpaired.fastq.gz DS70_Pl3-CRR995034.read2.paired.fastq.gz DS70_Pl3-CRR995034.read2.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 LB115_Br1-CRR995035_f1.fastq.gz LB115_Br1-CRR995035_r2.fastq.gz LB115_Br1-CRR995035.read1.paired.fastq.gz LB115_Br1-CRR995035.read1.unpaired.fastq.gz LB115_Br1-CRR995035.read2.paired.fastq.gz LB115_Br1-CRR995035.read2.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 LB115_Br2-CRR995036_f1.fastq.gz LB115_Br2-CRR995036_r2.fastq.gz LB115_Br2-CRR995036.read1.paired.fastq.gz LB115_Br2-CRR995036.read1.unpaired.fastq.gz LB115_Br2-CRR995036.read2.paired.fastq.gz LB115_Br2-CRR995036.read2.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 LB115_Br3-CRR995037_f1.fastq.gz LB115_Br3-CRR995037_r2.fastq.gz LB115_Br3-CRR995037.read1.paired.fastq.gz LB115_Br3-CRR995037.read1.unpaired.fastq.gz LB115_Br3-CRR995037.read2.paired.fastq.gz LB115_Br3-CRR995037.read2.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 LB115_Li1-CRR995038_f1.fastq.gz LB115_Li1-CRR995038_r2.fastq.gz LB115_Li1-CRR995038.read1.paired.fastq.gz LB115_Li1-CRR995038.read1.unpaired.fastq.gz LB115_Li1-CRR995038.read2.paired.fastq.gz LB115_Li1-CRR995038.read2.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 LB115_Li2-CRR995039_f1.fastq.gz LB115_Li2-CRR995039_r2.fastq.gz LB115_Li2-CRR995039.read1.paired.fastq.gz LB115_Li2-CRR995039.read1.unpaired.fastq.gz LB115_Li2-CRR995039.read2.paired.fastq.gz LB115_Li2-CRR995039.read2.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 LB115_Li3-CRR995040_f1.fastq.gz LB115_Li3-CRR995040_r2.fastq.gz LB115_Li3-CRR995040.read1.paired.fastq.gz LB115_Li3-CRR995040.read1.unpaired.fastq.gz LB115_Li3-CRR995040.read2.paired.fastq.gz LB115_Li3-CRR995040.read2.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 LB115_Mu1-CRR995041_f1.fastq.gz LB115_Mu1-CRR995041_r2.fastq.gz LB115_Mu1-CRR995041.read1.paired.fastq.gz LB115_Mu1-CRR995041.read1.unpaired.fastq.gz LB115_Mu1-CRR995041.read2.paired.fastq.gz LB115_Mu1-CRR995041.read2.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 LB115_Mu2-CRR995042_f1.fastq.gz LB115_Mu2-CRR995042_r2.fastq.gz LB115_Mu2-CRR995042.read1.paired.fastq.gz LB115_Mu2-CRR995042.read1.unpaired.fastq.gz LB115_Mu2-CRR995042.read2.paired.fastq.gz LB115_Mu2-CRR995042.read2.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 LB115_Mu3-CRR995043_f1.fastq.gz LB115_Mu3-CRR995043_r2.fastq.gz LB115_Mu3-CRR995043.read1.paired.fastq.gz LB115_Mu3-CRR995043.read1.unpaired.fastq.gz LB115_Mu3-CRR995043.read2.paired.fastq.gz LB115_Mu3-CRR995043.read2.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 LB168_F_Br2-CRR995044_f1.fastq.gz LB168_F_Br2-CRR995044_r2.fastq.gz LB168_F_Br2-CRR995044.read1.paired.fastq.gz LB168_F_Br2-CRR995044.read1.unpaired.fastq.gz LB168_F_Br2-CRR995044.read2.paired.fastq.gz LB168_F_Br2-CRR995044.read2.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 LB168_F_Li2-CRR995045_f1.fastq.gz LB168_F_Li2-CRR995045_r2.fastq.gz LB168_F_Li2-CRR995045.read1.paired.fastq.gz LB168_F_Li2-CRR995045.read1.unpaired.fastq.gz LB168_F_Li2-CRR995045.read2.paired.fastq.gz LB168_F_Li2-CRR995045.read2.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 LB168_F_Mu2-CRR995046_f1.fastq.gz LB168_F_Mu2-CRR995046_r2.fastq.gz LB168_F_Mu2-CRR995046.read1.paired.fastq.gz LB168_F_Mu2-CRR995046.read1.unpaired.fastq.gz LB168_F_Mu2-CRR995046.read2.paired.fastq.gz LB168_F_Mu2-CRR995046.read2.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 LB168_G_Br1-CRR995047_f1.fastq.gz LB168_G_Br1-CRR995047_r2.fastq.gz LB168_G_Br1-CRR995047.read1.paired.fastq.gz LB168_G_Br1-CRR995047.read1.unpaired.fastq.gz LB168_G_Br1-CRR995047.read2.paired.fastq.gz LB168_G_Br1-CRR995047.read2.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 LB168_G_Li1-CRR995048_f1.fastq.gz LB168_G_Li1-CRR995048_r2.fastq.gz LB168_G_Li1-CRR995048.read1.paired.fastq.gz LB168_G_Li1-CRR995048.read1.unpaired.fastq.gz LB168_G_Li1-CRR995048.read2.paired.fastq.gz LB168_G_Li1-CRR995048.read2.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 LB168_G_Mu1-CRR995049_f1.fastq.gz LB168_G_Mu1-CRR995049_r2.fastq.gz LB168_G_Mu1-CRR995049.read1.paired.fastq.gz LB168_G_Mu1-CRR995049.read1.unpaired.fastq.gz LB168_G_Mu1-CRR995049.read2.paired.fastq.gz LB168_G_Mu1-CRR995049.read2.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 LB168_H_Br3-CRR995050_f1.fastq.gz LB168_H_Br3-CRR995050_r2.fastq.gz LB168_H_Br3-CRR995050.read1.paired.fastq.gz LB168_H_Br3-CRR995050.read1.unpaired.fastq.gz LB168_H_Br3-CRR995050.read2.paired.fastq.gz LB168_H_Br3-CRR995050.read2.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 LB168_H_Li3-CRR995051_f1.fastq.gz LB168_H_Li3-CRR995051_r2.fastq.gz LB168_H_Li3-CRR995051.read1.paired.fastq.gz LB168_H_Li3-CRR995051.read1.unpaired.fastq.gz LB168_H_Li3-CRR995051.read2.paired.fastq.gz LB168_H_Li3-CRR995051.read2.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 LB168_H_Mu3-CRR995052_f1.fastq.gz LB168_H_Mu3-CRR995052_r2.fastq.gz LB168_H_Mu3-CRR995052.read1.paired.fastq.gz LB168_H_Mu3-CRR995052.read1.unpaired.fastq.gz LB168_H_Mu3-CRR995052.read2.paired.fastq.gz LB168_H_Mu3-CRR995052.read2.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 LB40_Br1-CRR995053_f1.fastq.gz LB40_Br1-CRR995053_r2.fastq.gz LB40_Br1-CRR995053.read1.paired.fastq.gz LB40_Br1-CRR995053.read1.unpaired.fastq.gz LB40_Br1-CRR995053.read2.paired.fastq.gz LB40_Br1-CRR995053.read2.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 LB40_Br3-CRR995055_f1.fastq.gz LB40_Br3-CRR995055_r2.fastq.gz LB40_Br3-CRR995055.read1.paired.fastq.gz LB40_Br3-CRR995055.read1.unpaired.fastq.gz LB40_Br3-CRR995055.read2.paired.fastq.gz LB40_Br3-CRR995055.read2.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 LB40_Li1-CRR995056_f1.fastq.gz LB40_Li1-CRR995056_r2.fastq.gz LB40_Li1-CRR995056.read1.paired.fastq.gz LB40_Li1-CRR995056.read1.unpaired.fastq.gz LB40_Li1-CRR995056.read2.paired.fastq.gz LB40_Li1-CRR995056.read2.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 LB40_Li2-CRR995057_f1.fastq.gz LB40_Li2-CRR995057_r2.fastq.gz LB40_Li2-CRR995057.read1.paired.fastq.gz LB40_Li2-CRR995057.read1.unpaired.fastq.gz LB40_Li2-CRR995057.read2.paired.fastq.gz LB40_Li2-CRR995057.read2.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 LB40_Li3-CRR995058_f1.fastq.gz LB40_Li3-CRR995058_r2.fastq.gz LB40_Li3-CRR995058.read1.paired.fastq.gz LB40_Li3-CRR995058.read1.unpaired.fastq.gz LB40_Li3-CRR995058.read2.paired.fastq.gz LB40_Li3-CRR995058.read2.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 LB40_Mu2-CRR995060_f1.fastq.gz LB40_Mu2-CRR995060_r2.fastq.gz LB40_Mu2-CRR995060.read1.paired.fastq.gz LB40_Mu2-CRR995060.read1.unpaired.fastq.gz LB40_Mu2-CRR995060.read2.paired.fastq.gz LB40_Mu2-CRR995060.read2.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 LB40_Mu3-CRR995061_f1.fastq.gz LB40_Mu3-CRR995061_r2.fastq.gz LB40_Mu3-CRR995061.read1.paired.fastq.gz LB40_Mu3-CRR995061.read1.unpaired.fastq.gz LB40_Mu3-CRR995061.read2.paired.fastq.gz LB40_Mu3-CRR995061.read2.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 LB40_Pl1-CRR995062_f1.fastq.gz LB40_Pl1-CRR995062_r2.fastq.gz LB40_Pl1-CRR995062.read1.paired.fastq.gz LB40_Pl1-CRR995062.read1.unpaired.fastq.gz LB40_Pl1-CRR995062.read2.paired.fastq.gz LB40_Pl1-CRR995062.read2.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 LB40_Pl2-CRR995063_f1.fastq.gz LB40_Pl2-CRR995063_r2.fastq.gz LB40_Pl2-CRR995063.read1.paired.fastq.gz LB40_Pl2-CRR995063.read1.unpaired.fastq.gz LB40_Pl2-CRR995063.read2.paired.fastq.gz LB40_Pl2-CRR995063.read2.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 LB40_Pl3-CRR995064_f1.fastq.gz LB40_Pl3-CRR995064_r2.fastq.gz LB40_Pl3-CRR995064.read1.paired.fastq.gz LB40_Pl3-CRR995064.read1.unpaired.fastq.gz LB40_Pl3-CRR995064.read2.paired.fastq.gz LB40_Pl3-CRR995064.read2.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 LB70_Br1-CRR995065_f1.fastq.gz LB70_Br1-CRR995065_r2.fastq.gz LB70_Br1-CRR995065.read1.paired.fastq.gz LB70_Br1-CRR995065.read1.unpaired.fastq.gz LB70_Br1-CRR995065.read2.paired.fastq.gz LB70_Br1-CRR995065.read2.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 LB70_Br2-CRR995066_f1.fastq.gz LB70_Br2-CRR995066_r2.fastq.gz LB70_Br2-CRR995066.read1.paired.fastq.gz LB70_Br2-CRR995066.read1.unpaired.fastq.gz LB70_Br2-CRR995066.read2.paired.fastq.gz LB70_Br2-CRR995066.read2.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 LB70_Br3-CRR995067_f1.fastq.gz LB70_Br3-CRR995067_r2.fastq.gz LB70_Br3-CRR995067.read1.paired.fastq.gz LB70_Br3-CRR995067.read1.unpaired.fastq.gz LB70_Br3-CRR995067.read2.paired.fastq.gz LB70_Br3-CRR995067.read2.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 LB70_Li1-CRR995068_f1.fastq.gz LB70_Li1-CRR995068_r2.fastq.gz LB70_Li1-CRR995068.read1.paired.fastq.gz LB70_Li1-CRR995068.read1.unpaired.fastq.gz LB70_Li1-CRR995068.read2.paired.fastq.gz LB70_Li1-CRR995068.read2.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 LB70_Li2-CRR995069_f1.fastq.gz LB70_Li2-CRR995069_r2.fastq.gz LB70_Li2-CRR995069.read1.paired.fastq.gz LB70_Li2-CRR995069.read1.unpaired.fastq.gz LB70_Li2-CRR995069.read2.paired.fastq.gz LB70_Li2-CRR995069.read2.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 LB70_Li3-CRR995070_f1.fastq.gz LB70_Li3-CRR995070_r2.fastq.gz LB70_Li3-CRR995070.read1.paired.fastq.gz LB70_Li3-CRR995070.read1.unpaired.fastq.gz LB70_Li3-CRR995070.read2.paired.fastq.gz LB70_Li3-CRR995070.read2.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 LB70_Mu1-CRR995071_f1.fastq.gz LB70_Mu1-CRR995071_r2.fastq.gz LB70_Mu1-CRR995071.read1.paired.fastq.gz LB70_Mu1-CRR995071.read1.unpaired.fastq.gz LB70_Mu1-CRR995071.read2.paired.fastq.gz LB70_Mu1-CRR995071.read2.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 LB70_Mu2-CRR995072_f1.fastq.gz LB70_Mu2-CRR995072_r2.fastq.gz LB70_Mu2-CRR995072.read1.paired.fastq.gz LB70_Mu2-CRR995072.read1.unpaired.fastq.gz LB70_Mu2-CRR995072.read2.paired.fastq.gz LB70_Mu2-CRR995072.read2.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 LB70_Mu3-CRR995073_f1.fastq.gz LB70_Mu3-CRR995073_r2.fastq.gz LB70_Mu3-CRR995073.read1.paired.fastq.gz LB70_Mu3-CRR995073.read1.unpaired.fastq.gz LB70_Mu3-CRR995073.read2.paired.fastq.gz LB70_Mu3-CRR995073.read2.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 LB70_Pl1-CRR995074_f1.fastq.gz LB70_Pl1-CRR995074_r2.fastq.gz LB70_Pl1-CRR995074.read1.paired.fastq.gz LB70_Pl1-CRR995074.read1.unpaired.fastq.gz LB70_Pl1-CRR995074.read2.paired.fastq.gz LB70_Pl1-CRR995074.read2.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 LB70_Pl2-CRR995075_f1.fastq.gz LB70_Pl2-CRR995075_r2.fastq.gz LB70_Pl2-CRR995075.read1.paired.fastq.gz LB70_Pl2-CRR995075.read1.unpaired.fastq.gz LB70_Pl2-CRR995075.read2.paired.fastq.gz LB70_Pl2-CRR995075.read2.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 LB70_Pl3-CRR995076_f1.fastq.gz LB70_Pl3-CRR995076_r2.fastq.gz LB70_Pl3-CRR995076.read1.paired.fastq.gz LB70_Pl3-CRR995076.read1.unpaired.fastq.gz LB70_Pl3-CRR995076.read2.paired.fastq.gz LB70_Pl3-CRR995076.read2.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 LS115_Br1-CRR995077_f1.fastq.gz LS115_Br1-CRR995077_r2.fastq.gz LS115_Br1-CRR995077.read1.paired.fastq.gz LS115_Br1-CRR995077.read1.unpaired.fastq.gz LS115_Br1-CRR995077.read2.paired.fastq.gz LS115_Br1-CRR995077.read2.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 LS115_Br2-CRR995078_f1.fastq.gz LS115_Br2-CRR995078_r2.fastq.gz LS115_Br2-CRR995078.read1.paired.fastq.gz LS115_Br2-CRR995078.read1.unpaired.fastq.gz LS115_Br2-CRR995078.read2.paired.fastq.gz LS115_Br2-CRR995078.read2.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 LS115_Br3-CRR995079_f1.fastq.gz LS115_Br3-CRR995079_r2.fastq.gz LS115_Br3-CRR995079.read1.paired.fastq.gz LS115_Br3-CRR995079.read1.unpaired.fastq.gz LS115_Br3-CRR995079.read2.paired.fastq.gz LS115_Br3-CRR995079.read2.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 LS115_Li1-CRR995080_f1.fastq.gz LS115_Li1-CRR995080_r2.fastq.gz LS115_Li1-CRR995080.read1.paired.fastq.gz LS115_Li1-CRR995080.read1.unpaired.fastq.gz LS115_Li1-CRR995080.read2.paired.fastq.gz LS115_Li1-CRR995080.read2.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 LS115_Li2-CRR995081_f1.fastq.gz LS115_Li2-CRR995081_r2.fastq.gz LS115_Li2-CRR995081.read1.paired.fastq.gz LS115_Li2-CRR995081.read1.unpaired.fastq.gz LS115_Li2-CRR995081.read2.paired.fastq.gz LS115_Li2-CRR995081.read2.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 LS115_Li3-CRR995082_f1.fastq.gz LS115_Li3-CRR995082_r2.fastq.gz LS115_Li3-CRR995082.read1.paired.fastq.gz LS115_Li3-CRR995082.read1.unpaired.fastq.gz LS115_Li3-CRR995082.read2.paired.fastq.gz LS115_Li3-CRR995082.read2.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 LS115_Mu1-CRR995083_f1.fastq.gz LS115_Mu1-CRR995083_r2.fastq.gz LS115_Mu1-CRR995083.read1.paired.fastq.gz LS115_Mu1-CRR995083.read1.unpaired.fastq.gz LS115_Mu1-CRR995083.read2.paired.fastq.gz LS115_Mu1-CRR995083.read2.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 LS115_Mu2-CRR995084_f1.fastq.gz LS115_Mu2-CRR995084_r2.fastq.gz LS115_Mu2-CRR995084.read1.paired.fastq.gz LS115_Mu2-CRR995084.read1.unpaired.fastq.gz LS115_Mu2-CRR995084.read2.paired.fastq.gz LS115_Mu2-CRR995084.read2.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 LS115_Mu3-CRR995085_f1.fastq.gz LS115_Mu3-CRR995085_r2.fastq.gz LS115_Mu3-CRR995085.read1.paired.fastq.gz LS115_Mu3-CRR995085.read1.unpaired.fastq.gz LS115_Mu3-CRR995085.read2.paired.fastq.gz LS115_Mu3-CRR995085.read2.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 LS168_B_Li1-CRR995087_f1.fastq.gz LS168_B_Li1-CRR995087_r2.fastq.gz LS168_B_Li1-CRR995087.read1.paired.fastq.gz LS168_B_Li1-CRR995087.read1.unpaired.fastq.gz LS168_B_Li1-CRR995087.read2.paired.fastq.gz LS168_B_Li1-CRR995087.read2.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 LS168_B_Mu1-CRR995088_f1.fastq.gz LS168_B_Mu1-CRR995088_r2.fastq.gz LS168_B_Mu1-CRR995088.read1.paired.fastq.gz LS168_B_Mu1-CRR995088.read1.unpaired.fastq.gz LS168_B_Mu1-CRR995088.read2.paired.fastq.gz LS168_B_Mu1-CRR995088.read2.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 LS168_C_Br2-CRR995089_f1.fastq.gz LS168_C_Br2-CRR995089_r2.fastq.gz LS168_C_Br2-CRR995089.read1.paired.fastq.gz LS168_C_Br2-CRR995089.read1.unpaired.fastq.gz LS168_C_Br2-CRR995089.read2.paired.fastq.gz LS168_C_Br2-CRR995089.read2.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 LS168_C_Li2-CRR995090_f1.fastq.gz LS168_C_Li2-CRR995090_r2.fastq.gz LS168_C_Li2-CRR995090.read1.paired.fastq.gz LS168_C_Li2-CRR995090.read1.unpaired.fastq.gz LS168_C_Li2-CRR995090.read2.paired.fastq.gz LS168_C_Li2-CRR995090.read2.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 LS168_C_Mu2-CRR995091_f1.fastq.gz LS168_C_Mu2-CRR995091_r2.fastq.gz LS168_C_Mu2-CRR995091.read1.paired.fastq.gz LS168_C_Mu2-CRR995091.read1.unpaired.fastq.gz LS168_C_Mu2-CRR995091.read2.paired.fastq.gz LS168_C_Mu2-CRR995091.read2.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 LS168_L_Li3-CRR995092_f1.fastq.gz LS168_L_Li3-CRR995092_r2.fastq.gz LS168_L_Li3-CRR995092.read1.paired.fastq.gz LS168_L_Li3-CRR995092.read1.unpaired.fastq.gz LS168_L_Li3-CRR995092.read2.paired.fastq.gz LS168_L_Li3-CRR995092.read2.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 LS40_Br2-CRR995095_f1.fastq.gz LS40_Br2-CRR995095_r2.fastq.gz LS40_Br2-CRR995095.read1.paired.fastq.gz LS40_Br2-CRR995095.read1.unpaired.fastq.gz LS40_Br2-CRR995095.read2.paired.fastq.gz LS40_Br2-CRR995095.read2.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 LS40_Br3-CRR995096_f1.fastq.gz LS40_Br3-CRR995096_r2.fastq.gz LS40_Br3-CRR995096.read1.paired.fastq.gz LS40_Br3-CRR995096.read1.unpaired.fastq.gz LS40_Br3-CRR995096.read2.paired.fastq.gz LS40_Br3-CRR995096.read2.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 LS40_Li1-CRR995097_f1.fastq.gz LS40_Li1-CRR995097_r2.fastq.gz LS40_Li1-CRR995097.read1.paired.fastq.gz LS40_Li1-CRR995097.read1.unpaired.fastq.gz LS40_Li1-CRR995097.read2.paired.fastq.gz LS40_Li1-CRR995097.read2.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 LS40_Li2-CRR995098_f1.fastq.gz LS40_Li2-CRR995098_r2.fastq.gz LS40_Li2-CRR995098.read1.paired.fastq.gz LS40_Li2-CRR995098.read1.unpaired.fastq.gz LS40_Li2-CRR995098.read2.paired.fastq.gz LS40_Li2-CRR995098.read2.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 LS40_Li3-CRR995099_f1.fastq.gz LS40_Li3-CRR995099_r2.fastq.gz LS40_Li3-CRR995099.read1.paired.fastq.gz LS40_Li3-CRR995099.read1.unpaired.fastq.gz LS40_Li3-CRR995099.read2.paired.fastq.gz LS40_Li3-CRR995099.read2.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 LS40_Mu1-CRR995100_f1.fastq.gz LS40_Mu1-CRR995100_r2.fastq.gz LS40_Mu1-CRR995100.read1.paired.fastq.gz LS40_Mu1-CRR995100.read1.unpaired.fastq.gz LS40_Mu1-CRR995100.read2.paired.fastq.gz LS40_Mu1-CRR995100.read2.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 LS40_Mu2-CRR995101_f1.fastq.gz LS40_Mu2-CRR995101_r2.fastq.gz LS40_Mu2-CRR995101.read1.paired.fastq.gz LS40_Mu2-CRR995101.read1.unpaired.fastq.gz LS40_Mu2-CRR995101.read2.paired.fastq.gz LS40_Mu2-CRR995101.read2.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 LS40_Mu3-CRR995102_f1.fastq.gz LS40_Mu3-CRR995102_r2.fastq.gz LS40_Mu3-CRR995102.read1.paired.fastq.gz LS40_Mu3-CRR995102.read1.unpaired.fastq.gz LS40_Mu3-CRR995102.read2.paired.fastq.gz LS40_Mu3-CRR995102.read2.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 LS40_Pl1-CRR995103_f1.fastq.gz LS40_Pl1-CRR995103_r2.fastq.gz LS40_Pl1-CRR995103.read1.paired.fastq.gz LS40_Pl1-CRR995103.read1.unpaired.fastq.gz LS40_Pl1-CRR995103.read2.paired.fastq.gz LS40_Pl1-CRR995103.read2.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 LS40_Pl2-CRR995104_f1.fastq.gz LS40_Pl2-CRR995104_r2.fastq.gz LS40_Pl2-CRR995104.read1.paired.fastq.gz LS40_Pl2-CRR995104.read1.unpaired.fastq.gz LS40_Pl2-CRR995104.read2.paired.fastq.gz LS40_Pl2-CRR995104.read2.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 LS40_Pl3-CRR995105_f1.fastq.gz LS40_Pl3-CRR995105_r2.fastq.gz LS40_Pl3-CRR995105.read1.paired.fastq.gz LS40_Pl3-CRR995105.read1.unpaired.fastq.gz LS40_Pl3-CRR995105.read2.paired.fastq.gz LS40_Pl3-CRR995105.read2.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 LS70_Br1-CRR995106_f1.fastq.gz LS70_Br1-CRR995106_r2.fastq.gz LS70_Br1-CRR995106.read1.paired.fastq.gz LS70_Br1-CRR995106.read1.unpaired.fastq.gz LS70_Br1-CRR995106.read2.paired.fastq.gz LS70_Br1-CRR995106.read2.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 LS70_Br2-CRR995107_f1.fastq.gz LS70_Br2-CRR995107_r2.fastq.gz LS70_Br2-CRR995107.read1.paired.fastq.gz LS70_Br2-CRR995107.read1.unpaired.fastq.gz LS70_Br2-CRR995107.read2.paired.fastq.gz LS70_Br2-CRR995107.read2.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 LS70_Br3-CRR995108_f1.fastq.gz LS70_Br3-CRR995108_r2.fastq.gz LS70_Br3-CRR995108.read1.paired.fastq.gz LS70_Br3-CRR995108.read1.unpaired.fastq.gz LS70_Br3-CRR995108.read2.paired.fastq.gz LS70_Br3-CRR995108.read2.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 LS70_Li1-CRR995109_f1.fastq.gz LS70_Li1-CRR995109_r2.fastq.gz LS70_Li1-CRR995109.read1.paired.fastq.gz LS70_Li1-CRR995109.read1.unpaired.fastq.gz LS70_Li1-CRR995109.read2.paired.fastq.gz LS70_Li1-CRR995109.read2.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 LS70_Li2-CRR995110_f1.fastq.gz LS70_Li2-CRR995110_r2.fastq.gz LS70_Li2-CRR995110.read1.paired.fastq.gz LS70_Li2-CRR995110.read1.unpaired.fastq.gz LS70_Li2-CRR995110.read2.paired.fastq.gz LS70_Li2-CRR995110.read2.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 LS70_Li3-CRR995111_f1.fastq.gz LS70_Li3-CRR995111_r2.fastq.gz LS70_Li3-CRR995111.read1.paired.fastq.gz LS70_Li3-CRR995111.read1.unpaired.fastq.gz LS70_Li3-CRR995111.read2.paired.fastq.gz LS70_Li3-CRR995111.read2.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 LS70_Mu1-CRR995112_f1.fastq.gz LS70_Mu1-CRR995112_r2.fastq.gz LS70_Mu1-CRR995112.read1.paired.fastq.gz LS70_Mu1-CRR995112.read1.unpaired.fastq.gz LS70_Mu1-CRR995112.read2.paired.fastq.gz LS70_Mu1-CRR995112.read2.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 LS70_Mu2-CRR995113_f1.fastq.gz LS70_Mu2-CRR995113_r2.fastq.gz LS70_Mu2-CRR995113.read1.paired.fastq.gz LS70_Mu2-CRR995113.read1.unpaired.fastq.gz LS70_Mu2-CRR995113.read2.paired.fastq.gz LS70_Mu2-CRR995113.read2.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 LS70_Mu3-CRR995114_f1.fastq.gz LS70_Mu3-CRR995114_r2.fastq.gz LS70_Mu3-CRR995114.read1.paired.fastq.gz LS70_Mu3-CRR995114.read1.unpaired.fastq.gz LS70_Mu3-CRR995114.read2.paired.fastq.gz LS70_Mu3-CRR995114.read2.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 LS70_Pl2-CRR995115_f1.fastq.gz LS70_Pl2-CRR995115_r2.fastq.gz LS70_Pl2-CRR995115.read1.paired.fastq.gz LS70_Pl2-CRR995115.read1.unpaired.fastq.gz LS70_Pl2-CRR995115.read2.paired.fastq.gz LS70_Pl2-CRR995115.read2.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 LS70_Pl3-CRR995116_f1.fastq.gz LS70_Pl3-CRR995116_r2.fastq.gz LS70_Pl3-CRR995116.read1.paired.fastq.gz LS70_Pl3-CRR995116.read1.unpaired.fastq.gz LS70_Pl3-CRR995116.read2.paired.fastq.gz LS70_Pl3-CRR995116.read2.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 &