/oak/stanford/groups/akundaje/marinovg/programs/trim_galore_v0.4.4/trim_galore --path_to_cutadapt ~/anaconda2/bin/cutadapt --clip_R1 9 --clip_R2 9 --three_prime_clip_r1 6 --three_prime_clip_r2 6 --paired ES159_Neural_Progenitors-SMF_MM_SMF_MM_NP_NO_R3.ERR4165151_1.fastq.10M_chunks0.gz ES159_Neural_Progenitors-SMF_MM_SMF_MM_NP_NO_R3.ERR4165151_2.fastq.10M_chunks0.gz
/oak/stanford/groups/akundaje/marinovg/programs/trim_galore_v0.4.4/trim_galore --path_to_cutadapt ~/anaconda2/bin/cutadapt --clip_R1 9 --clip_R2 9 --three_prime_clip_r1 6 --three_prime_clip_r2 6 --paired ES159_Neural_Progenitors-SMF_MM_SMF_MM_NP_NO_R3.ERR4165151_1.fastq.10M_chunks1.gz ES159_Neural_Progenitors-SMF_MM_SMF_MM_NP_NO_R3.ERR4165151_2.fastq.10M_chunks1.gz
/oak/stanford/groups/akundaje/marinovg/programs/trim_galore_v0.4.4/trim_galore --path_to_cutadapt ~/anaconda2/bin/cutadapt --clip_R1 9 --clip_R2 9 --three_prime_clip_r1 6 --three_prime_clip_r2 6 --paired ES159_Neural_Progenitors-SMF_MM_SMF_MM_NP_NO_R3.ERR4165151_1.fastq.10M_chunks10.gz ES159_Neural_Progenitors-SMF_MM_SMF_MM_NP_NO_R3.ERR4165151_2.fastq.10M_chunks10.gz
/oak/stanford/groups/akundaje/marinovg/programs/trim_galore_v0.4.4/trim_galore --path_to_cutadapt ~/anaconda2/bin/cutadapt --clip_R1 9 --clip_R2 9 --three_prime_clip_r1 6 --three_prime_clip_r2 6 --paired ES159_Neural_Progenitors-SMF_MM_SMF_MM_NP_NO_R3.ERR4165151_1.fastq.10M_chunks11.gz ES159_Neural_Progenitors-SMF_MM_SMF_MM_NP_NO_R3.ERR4165151_2.fastq.10M_chunks11.gz
/oak/stanford/groups/akundaje/marinovg/programs/trim_galore_v0.4.4/trim_galore --path_to_cutadapt ~/anaconda2/bin/cutadapt --clip_R1 9 --clip_R2 9 --three_prime_clip_r1 6 --three_prime_clip_r2 6 --paired ES159_Neural_Progenitors-SMF_MM_SMF_MM_NP_NO_R3.ERR4165151_1.fastq.10M_chunks12.gz ES159_Neural_Progenitors-SMF_MM_SMF_MM_NP_NO_R3.ERR4165151_2.fastq.10M_chunks12.gz
/oak/stanford/groups/akundaje/marinovg/programs/trim_galore_v0.4.4/trim_galore --path_to_cutadapt ~/anaconda2/bin/cutadapt --clip_R1 9 --clip_R2 9 --three_prime_clip_r1 6 --three_prime_clip_r2 6 --paired ES159_Neural_Progenitors-SMF_MM_SMF_MM_NP_NO_R3.ERR4165151_1.fastq.10M_chunks13.gz ES159_Neural_Progenitors-SMF_MM_SMF_MM_NP_NO_R3.ERR4165151_2.fastq.10M_chunks13.gz
/oak/stanford/groups/akundaje/marinovg/programs/trim_galore_v0.4.4/trim_galore --path_to_cutadapt ~/anaconda2/bin/cutadapt --clip_R1 9 --clip_R2 9 --three_prime_clip_r1 6 --three_prime_clip_r2 6 --paired ES159_Neural_Progenitors-SMF_MM_SMF_MM_NP_NO_R3.ERR4165151_1.fastq.10M_chunks14.gz ES159_Neural_Progenitors-SMF_MM_SMF_MM_NP_NO_R3.ERR4165151_2.fastq.10M_chunks14.gz
/oak/stanford/groups/akundaje/marinovg/programs/trim_galore_v0.4.4/trim_galore --path_to_cutadapt ~/anaconda2/bin/cutadapt --clip_R1 9 --clip_R2 9 --three_prime_clip_r1 6 --three_prime_clip_r2 6 --paired ES159_Neural_Progenitors-SMF_MM_SMF_MM_NP_NO_R3.ERR4165151_1.fastq.10M_chunks15.gz ES159_Neural_Progenitors-SMF_MM_SMF_MM_NP_NO_R3.ERR4165151_2.fastq.10M_chunks15.gz
/oak/stanford/groups/akundaje/marinovg/programs/trim_galore_v0.4.4/trim_galore --path_to_cutadapt ~/anaconda2/bin/cutadapt --clip_R1 9 --clip_R2 9 --three_prime_clip_r1 6 --three_prime_clip_r2 6 --paired ES159_Neural_Progenitors-SMF_MM_SMF_MM_NP_NO_R3.ERR4165151_1.fastq.10M_chunks16.gz ES159_Neural_Progenitors-SMF_MM_SMF_MM_NP_NO_R3.ERR4165151_2.fastq.10M_chunks16.gz
/oak/stanford/groups/akundaje/marinovg/programs/trim_galore_v0.4.4/trim_galore --path_to_cutadapt ~/anaconda2/bin/cutadapt --clip_R1 9 --clip_R2 9 --three_prime_clip_r1 6 --three_prime_clip_r2 6 --paired ES159_Neural_Progenitors-SMF_MM_SMF_MM_NP_NO_R3.ERR4165151_1.fastq.10M_chunks17.gz ES159_Neural_Progenitors-SMF_MM_SMF_MM_NP_NO_R3.ERR4165151_2.fastq.10M_chunks17.gz
/oak/stanford/groups/akundaje/marinovg/programs/trim_galore_v0.4.4/trim_galore --path_to_cutadapt ~/anaconda2/bin/cutadapt --clip_R1 9 --clip_R2 9 --three_prime_clip_r1 6 --three_prime_clip_r2 6 --paired ES159_Neural_Progenitors-SMF_MM_SMF_MM_NP_NO_R3.ERR4165151_1.fastq.10M_chunks18.gz ES159_Neural_Progenitors-SMF_MM_SMF_MM_NP_NO_R3.ERR4165151_2.fastq.10M_chunks18.gz
/oak/stanford/groups/akundaje/marinovg/programs/trim_galore_v0.4.4/trim_galore --path_to_cutadapt ~/anaconda2/bin/cutadapt --clip_R1 9 --clip_R2 9 --three_prime_clip_r1 6 --three_prime_clip_r2 6 --paired ES159_Neural_Progenitors-SMF_MM_SMF_MM_NP_NO_R3.ERR4165151_1.fastq.10M_chunks19.gz ES159_Neural_Progenitors-SMF_MM_SMF_MM_NP_NO_R3.ERR4165151_2.fastq.10M_chunks19.gz
/oak/stanford/groups/akundaje/marinovg/programs/trim_galore_v0.4.4/trim_galore --path_to_cutadapt ~/anaconda2/bin/cutadapt --clip_R1 9 --clip_R2 9 --three_prime_clip_r1 6 --three_prime_clip_r2 6 --paired ES159_Neural_Progenitors-SMF_MM_SMF_MM_NP_NO_R3.ERR4165151_1.fastq.10M_chunks2.gz ES159_Neural_Progenitors-SMF_MM_SMF_MM_NP_NO_R3.ERR4165151_2.fastq.10M_chunks2.gz
/oak/stanford/groups/akundaje/marinovg/programs/trim_galore_v0.4.4/trim_galore --path_to_cutadapt ~/anaconda2/bin/cutadapt --clip_R1 9 --clip_R2 9 --three_prime_clip_r1 6 --three_prime_clip_r2 6 --paired ES159_Neural_Progenitors-SMF_MM_SMF_MM_NP_NO_R3.ERR4165151_1.fastq.10M_chunks20.gz ES159_Neural_Progenitors-SMF_MM_SMF_MM_NP_NO_R3.ERR4165151_2.fastq.10M_chunks20.gz
/oak/stanford/groups/akundaje/marinovg/programs/trim_galore_v0.4.4/trim_galore --path_to_cutadapt ~/anaconda2/bin/cutadapt --clip_R1 9 --clip_R2 9 --three_prime_clip_r1 6 --three_prime_clip_r2 6 --paired ES159_Neural_Progenitors-SMF_MM_SMF_MM_NP_NO_R3.ERR4165151_1.fastq.10M_chunks21.gz ES159_Neural_Progenitors-SMF_MM_SMF_MM_NP_NO_R3.ERR4165151_2.fastq.10M_chunks21.gz
/oak/stanford/groups/akundaje/marinovg/programs/trim_galore_v0.4.4/trim_galore --path_to_cutadapt ~/anaconda2/bin/cutadapt --clip_R1 9 --clip_R2 9 --three_prime_clip_r1 6 --three_prime_clip_r2 6 --paired ES159_Neural_Progenitors-SMF_MM_SMF_MM_NP_NO_R3.ERR4165151_1.fastq.10M_chunks22.gz ES159_Neural_Progenitors-SMF_MM_SMF_MM_NP_NO_R3.ERR4165151_2.fastq.10M_chunks22.gz
/oak/stanford/groups/akundaje/marinovg/programs/trim_galore_v0.4.4/trim_galore --path_to_cutadapt ~/anaconda2/bin/cutadapt --clip_R1 9 --clip_R2 9 --three_prime_clip_r1 6 --three_prime_clip_r2 6 --paired ES159_Neural_Progenitors-SMF_MM_SMF_MM_NP_NO_R3.ERR4165151_1.fastq.10M_chunks23.gz ES159_Neural_Progenitors-SMF_MM_SMF_MM_NP_NO_R3.ERR4165151_2.fastq.10M_chunks23.gz
/oak/stanford/groups/akundaje/marinovg/programs/trim_galore_v0.4.4/trim_galore --path_to_cutadapt ~/anaconda2/bin/cutadapt --clip_R1 9 --clip_R2 9 --three_prime_clip_r1 6 --three_prime_clip_r2 6 --paired ES159_Neural_Progenitors-SMF_MM_SMF_MM_NP_NO_R3.ERR4165151_1.fastq.10M_chunks24.gz ES159_Neural_Progenitors-SMF_MM_SMF_MM_NP_NO_R3.ERR4165151_2.fastq.10M_chunks24.gz
/oak/stanford/groups/akundaje/marinovg/programs/trim_galore_v0.4.4/trim_galore --path_to_cutadapt ~/anaconda2/bin/cutadapt --clip_R1 9 --clip_R2 9 --three_prime_clip_r1 6 --three_prime_clip_r2 6 --paired ES159_Neural_Progenitors-SMF_MM_SMF_MM_NP_NO_R3.ERR4165151_1.fastq.10M_chunks25.gz ES159_Neural_Progenitors-SMF_MM_SMF_MM_NP_NO_R3.ERR4165151_2.fastq.10M_chunks25.gz
/oak/stanford/groups/akundaje/marinovg/programs/trim_galore_v0.4.4/trim_galore --path_to_cutadapt ~/anaconda2/bin/cutadapt --clip_R1 9 --clip_R2 9 --three_prime_clip_r1 6 --three_prime_clip_r2 6 --paired ES159_Neural_Progenitors-SMF_MM_SMF_MM_NP_NO_R3.ERR4165151_1.fastq.10M_chunks3.gz ES159_Neural_Progenitors-SMF_MM_SMF_MM_NP_NO_R3.ERR4165151_2.fastq.10M_chunks3.gz
/oak/stanford/groups/akundaje/marinovg/programs/trim_galore_v0.4.4/trim_galore --path_to_cutadapt ~/anaconda2/bin/cutadapt --clip_R1 9 --clip_R2 9 --three_prime_clip_r1 6 --three_prime_clip_r2 6 --paired ES159_Neural_Progenitors-SMF_MM_SMF_MM_NP_NO_R3.ERR4165151_1.fastq.10M_chunks4.gz ES159_Neural_Progenitors-SMF_MM_SMF_MM_NP_NO_R3.ERR4165151_2.fastq.10M_chunks4.gz
/oak/stanford/groups/akundaje/marinovg/programs/trim_galore_v0.4.4/trim_galore --path_to_cutadapt ~/anaconda2/bin/cutadapt --clip_R1 9 --clip_R2 9 --three_prime_clip_r1 6 --three_prime_clip_r2 6 --paired ES159_Neural_Progenitors-SMF_MM_SMF_MM_NP_NO_R3.ERR4165151_1.fastq.10M_chunks5.gz ES159_Neural_Progenitors-SMF_MM_SMF_MM_NP_NO_R3.ERR4165151_2.fastq.10M_chunks5.gz
/oak/stanford/groups/akundaje/marinovg/programs/trim_galore_v0.4.4/trim_galore --path_to_cutadapt ~/anaconda2/bin/cutadapt --clip_R1 9 --clip_R2 9 --three_prime_clip_r1 6 --three_prime_clip_r2 6 --paired ES159_Neural_Progenitors-SMF_MM_SMF_MM_NP_NO_R3.ERR4165151_1.fastq.10M_chunks6.gz ES159_Neural_Progenitors-SMF_MM_SMF_MM_NP_NO_R3.ERR4165151_2.fastq.10M_chunks6.gz
/oak/stanford/groups/akundaje/marinovg/programs/trim_galore_v0.4.4/trim_galore --path_to_cutadapt ~/anaconda2/bin/cutadapt --clip_R1 9 --clip_R2 9 --three_prime_clip_r1 6 --three_prime_clip_r2 6 --paired ES159_Neural_Progenitors-SMF_MM_SMF_MM_NP_NO_R3.ERR4165151_1.fastq.10M_chunks7.gz ES159_Neural_Progenitors-SMF_MM_SMF_MM_NP_NO_R3.ERR4165151_2.fastq.10M_chunks7.gz
/oak/stanford/groups/akundaje/marinovg/programs/trim_galore_v0.4.4/trim_galore --path_to_cutadapt ~/anaconda2/bin/cutadapt --clip_R1 9 --clip_R2 9 --three_prime_clip_r1 6 --three_prime_clip_r2 6 --paired ES159_Neural_Progenitors-SMF_MM_SMF_MM_NP_NO_R3.ERR4165151_1.fastq.10M_chunks8.gz ES159_Neural_Progenitors-SMF_MM_SMF_MM_NP_NO_R3.ERR4165151_2.fastq.10M_chunks8.gz
/oak/stanford/groups/akundaje/marinovg/programs/trim_galore_v0.4.4/trim_galore --path_to_cutadapt ~/anaconda2/bin/cutadapt --clip_R1 9 --clip_R2 9 --three_prime_clip_r1 6 --three_prime_clip_r2 6 --paired ES159_Neural_Progenitors-SMF_MM_SMF_MM_NP_NO_R3.ERR4165151_1.fastq.10M_chunks9.gz ES159_Neural_Progenitors-SMF_MM_SMF_MM_NP_NO_R3.ERR4165151_2.fastq.10M_chunks9.gz
/oak/stanford/groups/akundaje/marinovg/programs/trim_galore_v0.4.4/trim_galore --path_to_cutadapt ~/anaconda2/bin/cutadapt --clip_R1 9 --clip_R2 9 --three_prime_clip_r1 6 --three_prime_clip_r2 6 --paired ES159_Neural_Progenitors-SMF_MM_SMF_MM_NP_NO_R4.ERR4165146_1.fastq.10M_chunks0.gz ES159_Neural_Progenitors-SMF_MM_SMF_MM_NP_NO_R4.ERR4165146_2.fastq.10M_chunks0.gz
/oak/stanford/groups/akundaje/marinovg/programs/trim_galore_v0.4.4/trim_galore --path_to_cutadapt ~/anaconda2/bin/cutadapt --clip_R1 9 --clip_R2 9 --three_prime_clip_r1 6 --three_prime_clip_r2 6 --paired ES159_Neural_Progenitors-SMF_MM_SMF_MM_NP_NO_R4.ERR4165146_1.fastq.10M_chunks1.gz ES159_Neural_Progenitors-SMF_MM_SMF_MM_NP_NO_R4.ERR4165146_2.fastq.10M_chunks1.gz
/oak/stanford/groups/akundaje/marinovg/programs/trim_galore_v0.4.4/trim_galore --path_to_cutadapt ~/anaconda2/bin/cutadapt --clip_R1 9 --clip_R2 9 --three_prime_clip_r1 6 --three_prime_clip_r2 6 --paired ES159_Neural_Progenitors-SMF_MM_SMF_MM_NP_NO_R4.ERR4165146_1.fastq.10M_chunks10.gz ES159_Neural_Progenitors-SMF_MM_SMF_MM_NP_NO_R4.ERR4165146_2.fastq.10M_chunks10.gz
/oak/stanford/groups/akundaje/marinovg/programs/trim_galore_v0.4.4/trim_galore --path_to_cutadapt ~/anaconda2/bin/cutadapt --clip_R1 9 --clip_R2 9 --three_prime_clip_r1 6 --three_prime_clip_r2 6 --paired ES159_Neural_Progenitors-SMF_MM_SMF_MM_NP_NO_R4.ERR4165146_1.fastq.10M_chunks11.gz ES159_Neural_Progenitors-SMF_MM_SMF_MM_NP_NO_R4.ERR4165146_2.fastq.10M_chunks11.gz
/oak/stanford/groups/akundaje/marinovg/programs/trim_galore_v0.4.4/trim_galore --path_to_cutadapt ~/anaconda2/bin/cutadapt --clip_R1 9 --clip_R2 9 --three_prime_clip_r1 6 --three_prime_clip_r2 6 --paired ES159_Neural_Progenitors-SMF_MM_SMF_MM_NP_NO_R4.ERR4165146_1.fastq.10M_chunks12.gz ES159_Neural_Progenitors-SMF_MM_SMF_MM_NP_NO_R4.ERR4165146_2.fastq.10M_chunks12.gz
/oak/stanford/groups/akundaje/marinovg/programs/trim_galore_v0.4.4/trim_galore --path_to_cutadapt ~/anaconda2/bin/cutadapt --clip_R1 9 --clip_R2 9 --three_prime_clip_r1 6 --three_prime_clip_r2 6 --paired ES159_Neural_Progenitors-SMF_MM_SMF_MM_NP_NO_R4.ERR4165146_1.fastq.10M_chunks13.gz ES159_Neural_Progenitors-SMF_MM_SMF_MM_NP_NO_R4.ERR4165146_2.fastq.10M_chunks13.gz
/oak/stanford/groups/akundaje/marinovg/programs/trim_galore_v0.4.4/trim_galore --path_to_cutadapt ~/anaconda2/bin/cutadapt --clip_R1 9 --clip_R2 9 --three_prime_clip_r1 6 --three_prime_clip_r2 6 --paired ES159_Neural_Progenitors-SMF_MM_SMF_MM_NP_NO_R4.ERR4165146_1.fastq.10M_chunks14.gz ES159_Neural_Progenitors-SMF_MM_SMF_MM_NP_NO_R4.ERR4165146_2.fastq.10M_chunks14.gz
/oak/stanford/groups/akundaje/marinovg/programs/trim_galore_v0.4.4/trim_galore --path_to_cutadapt ~/anaconda2/bin/cutadapt --clip_R1 9 --clip_R2 9 --three_prime_clip_r1 6 --three_prime_clip_r2 6 --paired ES159_Neural_Progenitors-SMF_MM_SMF_MM_NP_NO_R4.ERR4165146_1.fastq.10M_chunks15.gz ES159_Neural_Progenitors-SMF_MM_SMF_MM_NP_NO_R4.ERR4165146_2.fastq.10M_chunks15.gz
/oak/stanford/groups/akundaje/marinovg/programs/trim_galore_v0.4.4/trim_galore --path_to_cutadapt ~/anaconda2/bin/cutadapt --clip_R1 9 --clip_R2 9 --three_prime_clip_r1 6 --three_prime_clip_r2 6 --paired ES159_Neural_Progenitors-SMF_MM_SMF_MM_NP_NO_R4.ERR4165146_1.fastq.10M_chunks16.gz ES159_Neural_Progenitors-SMF_MM_SMF_MM_NP_NO_R4.ERR4165146_2.fastq.10M_chunks16.gz
/oak/stanford/groups/akundaje/marinovg/programs/trim_galore_v0.4.4/trim_galore --path_to_cutadapt ~/anaconda2/bin/cutadapt --clip_R1 9 --clip_R2 9 --three_prime_clip_r1 6 --three_prime_clip_r2 6 --paired ES159_Neural_Progenitors-SMF_MM_SMF_MM_NP_NO_R4.ERR4165146_1.fastq.10M_chunks17.gz ES159_Neural_Progenitors-SMF_MM_SMF_MM_NP_NO_R4.ERR4165146_2.fastq.10M_chunks17.gz
/oak/stanford/groups/akundaje/marinovg/programs/trim_galore_v0.4.4/trim_galore --path_to_cutadapt ~/anaconda2/bin/cutadapt --clip_R1 9 --clip_R2 9 --three_prime_clip_r1 6 --three_prime_clip_r2 6 --paired ES159_Neural_Progenitors-SMF_MM_SMF_MM_NP_NO_R4.ERR4165146_1.fastq.10M_chunks18.gz ES159_Neural_Progenitors-SMF_MM_SMF_MM_NP_NO_R4.ERR4165146_2.fastq.10M_chunks18.gz
/oak/stanford/groups/akundaje/marinovg/programs/trim_galore_v0.4.4/trim_galore --path_to_cutadapt ~/anaconda2/bin/cutadapt --clip_R1 9 --clip_R2 9 --three_prime_clip_r1 6 --three_prime_clip_r2 6 --paired ES159_Neural_Progenitors-SMF_MM_SMF_MM_NP_NO_R4.ERR4165146_1.fastq.10M_chunks19.gz ES159_Neural_Progenitors-SMF_MM_SMF_MM_NP_NO_R4.ERR4165146_2.fastq.10M_chunks19.gz
/oak/stanford/groups/akundaje/marinovg/programs/trim_galore_v0.4.4/trim_galore --path_to_cutadapt ~/anaconda2/bin/cutadapt --clip_R1 9 --clip_R2 9 --three_prime_clip_r1 6 --three_prime_clip_r2 6 --paired ES159_Neural_Progenitors-SMF_MM_SMF_MM_NP_NO_R4.ERR4165146_1.fastq.10M_chunks2.gz ES159_Neural_Progenitors-SMF_MM_SMF_MM_NP_NO_R4.ERR4165146_2.fastq.10M_chunks2.gz
/oak/stanford/groups/akundaje/marinovg/programs/trim_galore_v0.4.4/trim_galore --path_to_cutadapt ~/anaconda2/bin/cutadapt --clip_R1 9 --clip_R2 9 --three_prime_clip_r1 6 --three_prime_clip_r2 6 --paired ES159_Neural_Progenitors-SMF_MM_SMF_MM_NP_NO_R4.ERR4165146_1.fastq.10M_chunks20.gz ES159_Neural_Progenitors-SMF_MM_SMF_MM_NP_NO_R4.ERR4165146_2.fastq.10M_chunks20.gz
/oak/stanford/groups/akundaje/marinovg/programs/trim_galore_v0.4.4/trim_galore --path_to_cutadapt ~/anaconda2/bin/cutadapt --clip_R1 9 --clip_R2 9 --three_prime_clip_r1 6 --three_prime_clip_r2 6 --paired ES159_Neural_Progenitors-SMF_MM_SMF_MM_NP_NO_R4.ERR4165146_1.fastq.10M_chunks21.gz ES159_Neural_Progenitors-SMF_MM_SMF_MM_NP_NO_R4.ERR4165146_2.fastq.10M_chunks21.gz
/oak/stanford/groups/akundaje/marinovg/programs/trim_galore_v0.4.4/trim_galore --path_to_cutadapt ~/anaconda2/bin/cutadapt --clip_R1 9 --clip_R2 9 --three_prime_clip_r1 6 --three_prime_clip_r2 6 --paired ES159_Neural_Progenitors-SMF_MM_SMF_MM_NP_NO_R4.ERR4165146_1.fastq.10M_chunks22.gz ES159_Neural_Progenitors-SMF_MM_SMF_MM_NP_NO_R4.ERR4165146_2.fastq.10M_chunks22.gz
/oak/stanford/groups/akundaje/marinovg/programs/trim_galore_v0.4.4/trim_galore --path_to_cutadapt ~/anaconda2/bin/cutadapt --clip_R1 9 --clip_R2 9 --three_prime_clip_r1 6 --three_prime_clip_r2 6 --paired ES159_Neural_Progenitors-SMF_MM_SMF_MM_NP_NO_R4.ERR4165146_1.fastq.10M_chunks23.gz ES159_Neural_Progenitors-SMF_MM_SMF_MM_NP_NO_R4.ERR4165146_2.fastq.10M_chunks23.gz
/oak/stanford/groups/akundaje/marinovg/programs/trim_galore_v0.4.4/trim_galore --path_to_cutadapt ~/anaconda2/bin/cutadapt --clip_R1 9 --clip_R2 9 --three_prime_clip_r1 6 --three_prime_clip_r2 6 --paired ES159_Neural_Progenitors-SMF_MM_SMF_MM_NP_NO_R4.ERR4165146_1.fastq.10M_chunks24.gz ES159_Neural_Progenitors-SMF_MM_SMF_MM_NP_NO_R4.ERR4165146_2.fastq.10M_chunks24.gz
/oak/stanford/groups/akundaje/marinovg/programs/trim_galore_v0.4.4/trim_galore --path_to_cutadapt ~/anaconda2/bin/cutadapt --clip_R1 9 --clip_R2 9 --three_prime_clip_r1 6 --three_prime_clip_r2 6 --paired ES159_Neural_Progenitors-SMF_MM_SMF_MM_NP_NO_R4.ERR4165146_1.fastq.10M_chunks25.gz ES159_Neural_Progenitors-SMF_MM_SMF_MM_NP_NO_R4.ERR4165146_2.fastq.10M_chunks25.gz
/oak/stanford/groups/akundaje/marinovg/programs/trim_galore_v0.4.4/trim_galore --path_to_cutadapt ~/anaconda2/bin/cutadapt --clip_R1 9 --clip_R2 9 --three_prime_clip_r1 6 --three_prime_clip_r2 6 --paired ES159_Neural_Progenitors-SMF_MM_SMF_MM_NP_NO_R4.ERR4165146_1.fastq.10M_chunks26.gz ES159_Neural_Progenitors-SMF_MM_SMF_MM_NP_NO_R4.ERR4165146_2.fastq.10M_chunks26.gz
/oak/stanford/groups/akundaje/marinovg/programs/trim_galore_v0.4.4/trim_galore --path_to_cutadapt ~/anaconda2/bin/cutadapt --clip_R1 9 --clip_R2 9 --three_prime_clip_r1 6 --three_prime_clip_r2 6 --paired ES159_Neural_Progenitors-SMF_MM_SMF_MM_NP_NO_R4.ERR4165146_1.fastq.10M_chunks3.gz ES159_Neural_Progenitors-SMF_MM_SMF_MM_NP_NO_R4.ERR4165146_2.fastq.10M_chunks3.gz
/oak/stanford/groups/akundaje/marinovg/programs/trim_galore_v0.4.4/trim_galore --path_to_cutadapt ~/anaconda2/bin/cutadapt --clip_R1 9 --clip_R2 9 --three_prime_clip_r1 6 --three_prime_clip_r2 6 --paired ES159_Neural_Progenitors-SMF_MM_SMF_MM_NP_NO_R4.ERR4165146_1.fastq.10M_chunks4.gz ES159_Neural_Progenitors-SMF_MM_SMF_MM_NP_NO_R4.ERR4165146_2.fastq.10M_chunks4.gz
/oak/stanford/groups/akundaje/marinovg/programs/trim_galore_v0.4.4/trim_galore --path_to_cutadapt ~/anaconda2/bin/cutadapt --clip_R1 9 --clip_R2 9 --three_prime_clip_r1 6 --three_prime_clip_r2 6 --paired ES159_Neural_Progenitors-SMF_MM_SMF_MM_NP_NO_R4.ERR4165146_1.fastq.10M_chunks5.gz ES159_Neural_Progenitors-SMF_MM_SMF_MM_NP_NO_R4.ERR4165146_2.fastq.10M_chunks5.gz
/oak/stanford/groups/akundaje/marinovg/programs/trim_galore_v0.4.4/trim_galore --path_to_cutadapt ~/anaconda2/bin/cutadapt --clip_R1 9 --clip_R2 9 --three_prime_clip_r1 6 --three_prime_clip_r2 6 --paired ES159_Neural_Progenitors-SMF_MM_SMF_MM_NP_NO_R4.ERR4165146_1.fastq.10M_chunks6.gz ES159_Neural_Progenitors-SMF_MM_SMF_MM_NP_NO_R4.ERR4165146_2.fastq.10M_chunks6.gz
/oak/stanford/groups/akundaje/marinovg/programs/trim_galore_v0.4.4/trim_galore --path_to_cutadapt ~/anaconda2/bin/cutadapt --clip_R1 9 --clip_R2 9 --three_prime_clip_r1 6 --three_prime_clip_r2 6 --paired ES159_Neural_Progenitors-SMF_MM_SMF_MM_NP_NO_R4.ERR4165146_1.fastq.10M_chunks7.gz ES159_Neural_Progenitors-SMF_MM_SMF_MM_NP_NO_R4.ERR4165146_2.fastq.10M_chunks7.gz
/oak/stanford/groups/akundaje/marinovg/programs/trim_galore_v0.4.4/trim_galore --path_to_cutadapt ~/anaconda2/bin/cutadapt --clip_R1 9 --clip_R2 9 --three_prime_clip_r1 6 --three_prime_clip_r2 6 --paired ES159_Neural_Progenitors-SMF_MM_SMF_MM_NP_NO_R4.ERR4165146_1.fastq.10M_chunks8.gz ES159_Neural_Progenitors-SMF_MM_SMF_MM_NP_NO_R4.ERR4165146_2.fastq.10M_chunks8.gz
/oak/stanford/groups/akundaje/marinovg/programs/trim_galore_v0.4.4/trim_galore --path_to_cutadapt ~/anaconda2/bin/cutadapt --clip_R1 9 --clip_R2 9 --three_prime_clip_r1 6 --three_prime_clip_r2 6 --paired ES159_Neural_Progenitors-SMF_MM_SMF_MM_NP_NO_R4.ERR4165146_1.fastq.10M_chunks9.gz ES159_Neural_Progenitors-SMF_MM_SMF_MM_NP_NO_R4.ERR4165146_2.fastq.10M_chunks9.gz
/oak/stanford/groups/akundaje/marinovg/programs/trim_galore_v0.4.4/trim_galore --path_to_cutadapt ~/anaconda2/bin/cutadapt --clip_R1 9 --clip_R2 9 --three_prime_clip_r1 6 --three_prime_clip_r2 6 --paired ES159-SMF_MM_ES_NO_R1.ERR4165153_1.fastq.10M_chunks0.gz ES159-SMF_MM_ES_NO_R1.ERR4165153_2.fastq.10M_chunks0.gz
/oak/stanford/groups/akundaje/marinovg/programs/trim_galore_v0.4.4/trim_galore --path_to_cutadapt ~/anaconda2/bin/cutadapt --clip_R1 9 --clip_R2 9 --three_prime_clip_r1 6 --three_prime_clip_r2 6 --paired ES159-SMF_MM_ES_NO_R1.ERR4165153_1.fastq.10M_chunks1.gz ES159-SMF_MM_ES_NO_R1.ERR4165153_2.fastq.10M_chunks1.gz
/oak/stanford/groups/akundaje/marinovg/programs/trim_galore_v0.4.4/trim_galore --path_to_cutadapt ~/anaconda2/bin/cutadapt --clip_R1 9 --clip_R2 9 --three_prime_clip_r1 6 --three_prime_clip_r2 6 --paired ES159-SMF_MM_ES_NO_R1.ERR4165153_1.fastq.10M_chunks2.gz ES159-SMF_MM_ES_NO_R1.ERR4165153_2.fastq.10M_chunks2.gz
/oak/stanford/groups/akundaje/marinovg/programs/trim_galore_v0.4.4/trim_galore --path_to_cutadapt ~/anaconda2/bin/cutadapt --clip_R1 9 --clip_R2 9 --three_prime_clip_r1 6 --three_prime_clip_r2 6 --paired ES159-SMF_MM_ES_NO_R1.ERR4165153_1.fastq.10M_chunks3.gz ES159-SMF_MM_ES_NO_R1.ERR4165153_2.fastq.10M_chunks3.gz
/oak/stanford/groups/akundaje/marinovg/programs/trim_galore_v0.4.4/trim_galore --path_to_cutadapt ~/anaconda2/bin/cutadapt --clip_R1 9 --clip_R2 9 --three_prime_clip_r1 6 --three_prime_clip_r2 6 --paired ES159-SMF_MM_ES_NO_R2.ERR4165147_1.fastq.10M_chunks0.gz ES159-SMF_MM_ES_NO_R2.ERR4165147_2.fastq.10M_chunks0.gz
/oak/stanford/groups/akundaje/marinovg/programs/trim_galore_v0.4.4/trim_galore --path_to_cutadapt ~/anaconda2/bin/cutadapt --clip_R1 9 --clip_R2 9 --three_prime_clip_r1 6 --three_prime_clip_r2 6 --paired ES159-SMF_MM_ES_NO_R2.ERR4165147_1.fastq.10M_chunks1.gz ES159-SMF_MM_ES_NO_R2.ERR4165147_2.fastq.10M_chunks1.gz
/oak/stanford/groups/akundaje/marinovg/programs/trim_galore_v0.4.4/trim_galore --path_to_cutadapt ~/anaconda2/bin/cutadapt --clip_R1 9 --clip_R2 9 --three_prime_clip_r1 6 --three_prime_clip_r2 6 --paired ES159-SMF_MM_ES_NO_R2.ERR4165147_1.fastq.10M_chunks10.gz ES159-SMF_MM_ES_NO_R2.ERR4165147_2.fastq.10M_chunks10.gz
/oak/stanford/groups/akundaje/marinovg/programs/trim_galore_v0.4.4/trim_galore --path_to_cutadapt ~/anaconda2/bin/cutadapt --clip_R1 9 --clip_R2 9 --three_prime_clip_r1 6 --three_prime_clip_r2 6 --paired ES159-SMF_MM_ES_NO_R2.ERR4165147_1.fastq.10M_chunks2.gz ES159-SMF_MM_ES_NO_R2.ERR4165147_2.fastq.10M_chunks2.gz
/oak/stanford/groups/akundaje/marinovg/programs/trim_galore_v0.4.4/trim_galore --path_to_cutadapt ~/anaconda2/bin/cutadapt --clip_R1 9 --clip_R2 9 --three_prime_clip_r1 6 --three_prime_clip_r2 6 --paired ES159-SMF_MM_ES_NO_R2.ERR4165147_1.fastq.10M_chunks3.gz ES159-SMF_MM_ES_NO_R2.ERR4165147_2.fastq.10M_chunks3.gz
/oak/stanford/groups/akundaje/marinovg/programs/trim_galore_v0.4.4/trim_galore --path_to_cutadapt ~/anaconda2/bin/cutadapt --clip_R1 9 --clip_R2 9 --three_prime_clip_r1 6 --three_prime_clip_r2 6 --paired ES159-SMF_MM_ES_NO_R2.ERR4165147_1.fastq.10M_chunks4.gz ES159-SMF_MM_ES_NO_R2.ERR4165147_2.fastq.10M_chunks4.gz
/oak/stanford/groups/akundaje/marinovg/programs/trim_galore_v0.4.4/trim_galore --path_to_cutadapt ~/anaconda2/bin/cutadapt --clip_R1 9 --clip_R2 9 --three_prime_clip_r1 6 --three_prime_clip_r2 6 --paired ES159-SMF_MM_ES_NO_R2.ERR4165147_1.fastq.10M_chunks5.gz ES159-SMF_MM_ES_NO_R2.ERR4165147_2.fastq.10M_chunks5.gz
/oak/stanford/groups/akundaje/marinovg/programs/trim_galore_v0.4.4/trim_galore --path_to_cutadapt ~/anaconda2/bin/cutadapt --clip_R1 9 --clip_R2 9 --three_prime_clip_r1 6 --three_prime_clip_r2 6 --paired ES159-SMF_MM_ES_NO_R2.ERR4165147_1.fastq.10M_chunks6.gz ES159-SMF_MM_ES_NO_R2.ERR4165147_2.fastq.10M_chunks6.gz
/oak/stanford/groups/akundaje/marinovg/programs/trim_galore_v0.4.4/trim_galore --path_to_cutadapt ~/anaconda2/bin/cutadapt --clip_R1 9 --clip_R2 9 --three_prime_clip_r1 6 --three_prime_clip_r2 6 --paired ES159-SMF_MM_ES_NO_R2.ERR4165147_1.fastq.10M_chunks7.gz ES159-SMF_MM_ES_NO_R2.ERR4165147_2.fastq.10M_chunks7.gz
/oak/stanford/groups/akundaje/marinovg/programs/trim_galore_v0.4.4/trim_galore --path_to_cutadapt ~/anaconda2/bin/cutadapt --clip_R1 9 --clip_R2 9 --three_prime_clip_r1 6 --three_prime_clip_r2 6 --paired ES159-SMF_MM_ES_NO_R2.ERR4165147_1.fastq.10M_chunks8.gz ES159-SMF_MM_ES_NO_R2.ERR4165147_2.fastq.10M_chunks8.gz
/oak/stanford/groups/akundaje/marinovg/programs/trim_galore_v0.4.4/trim_galore --path_to_cutadapt ~/anaconda2/bin/cutadapt --clip_R1 9 --clip_R2 9 --three_prime_clip_r1 6 --three_prime_clip_r2 6 --paired ES159-SMF_MM_ES_NO_R2.ERR4165147_1.fastq.10M_chunks9.gz ES159-SMF_MM_ES_NO_R2.ERR4165147_2.fastq.10M_chunks9.gz
/oak/stanford/groups/akundaje/marinovg/programs/trim_galore_v0.4.4/trim_galore --path_to_cutadapt ~/anaconda2/bin/cutadapt --clip_R1 9 --clip_R2 9 --three_prime_clip_r1 6 --three_prime_clip_r2 6 --paired ES_NO_P1_R1.ERR4078800_1.fastq.10M_chunks0.gz ES_NO_P1_R1.ERR4078800_2.fastq.10M_chunks0.gz
/oak/stanford/groups/akundaje/marinovg/programs/trim_galore_v0.4.4/trim_galore --path_to_cutadapt ~/anaconda2/bin/cutadapt --clip_R1 9 --clip_R2 9 --three_prime_clip_r1 6 --three_prime_clip_r2 6 --paired ES_NO_P1_R2.ERR4078790_1.fastq.10M_chunks0.gz ES_NO_P1_R2.ERR4078790_2.fastq.10M_chunks0.gz
/oak/stanford/groups/akundaje/marinovg/programs/trim_galore_v0.4.4/trim_galore --path_to_cutadapt ~/anaconda2/bin/cutadapt --clip_R1 9 --clip_R2 9 --three_prime_clip_r1 6 --three_prime_clip_r2 6 --paired RESTKO_NO_P1_R1.ERR4078793_1.fastq.10M_chunks0.gz RESTKO_NO_P1_R1.ERR4078793_2.fastq.10M_chunks0.gz
/oak/stanford/groups/akundaje/marinovg/programs/trim_galore_v0.4.4/trim_galore --path_to_cutadapt ~/anaconda2/bin/cutadapt --clip_R1 9 --clip_R2 9 --three_prime_clip_r1 6 --three_prime_clip_r2 6 --paired RESTKO_NO_P1_R2.ERR4078798_1.fastq.10M_chunks0.gz RESTKO_NO_P1_R2.ERR4078798_2.fastq.10M_chunks0.gz
/oak/stanford/groups/akundaje/marinovg/programs/trim_galore_v0.4.4/trim_galore --path_to_cutadapt ~/anaconda2/bin/cutadapt --clip_R1 9 --clip_R2 9 --three_prime_clip_r1 6 --three_prime_clip_r2 6 --paired TKO_DE_P1_R1.ERR4078787_1.fastq.10M_chunks0.gz TKO_DE_P1_R1.ERR4078787_2.fastq.10M_chunks0.gz
/oak/stanford/groups/akundaje/marinovg/programs/trim_galore_v0.4.4/trim_galore --path_to_cutadapt ~/anaconda2/bin/cutadapt --clip_R1 9 --clip_R2 9 --three_prime_clip_r1 6 --three_prime_clip_r2 6 --paired TKO_DE_P1_R1.ERR4078792_1.fastq.10M_chunks0.gz TKO_DE_P1_R1.ERR4078792_2.fastq.10M_chunks0.gz
/oak/stanford/groups/akundaje/marinovg/programs/trim_galore_v0.4.4/trim_galore --path_to_cutadapt ~/anaconda2/bin/cutadapt --clip_R1 9 --clip_R2 9 --three_prime_clip_r1 6 --three_prime_clip_r2 6 --paired TKO_DE_P2_R1.ERR4078784_1.fastq.10M_chunks0.gz TKO_DE_P2_R1.ERR4078784_2.fastq.10M_chunks0.gz
/oak/stanford/groups/akundaje/marinovg/programs/trim_galore_v0.4.4/trim_galore --path_to_cutadapt ~/anaconda2/bin/cutadapt --clip_R1 9 --clip_R2 9 --three_prime_clip_r1 6 --three_prime_clip_r2 6 --paired TKO_DE_P2_R2.ERR4078785_1.fastq.10M_chunks0.gz TKO_DE_P2_R2.ERR4078785_2.fastq.10M_chunks0.gz
/oak/stanford/groups/akundaje/marinovg/programs/trim_galore_v0.4.4/trim_galore --path_to_cutadapt ~/anaconda2/bin/cutadapt --clip_R1 9 --clip_R2 9 --three_prime_clip_r1 6 --three_prime_clip_r2 6 --paired TKO_DE_P3_R1.ERR4078791_1.fastq.10M_chunks0.gz TKO_DE_P3_R1.ERR4078791_2.fastq.10M_chunks0.gz
/oak/stanford/groups/akundaje/marinovg/programs/trim_galore_v0.4.4/trim_galore --path_to_cutadapt ~/anaconda2/bin/cutadapt --clip_R1 9 --clip_R2 9 --three_prime_clip_r1 6 --three_prime_clip_r2 6 --paired TKO_DE_P3_R2.ERR4078783_1.fastq.10M_chunks0.gz TKO_DE_P3_R2.ERR4078783_2.fastq.10M_chunks0.gz
/oak/stanford/groups/akundaje/marinovg/programs/trim_galore_v0.4.4/trim_galore --path_to_cutadapt ~/anaconda2/bin/cutadapt --clip_R1 9 --clip_R2 9 --three_prime_clip_r1 6 --three_prime_clip_r2 6 --paired TKO_ES159-SMF_MM_TKO_DE_R1.ERR4165150_1.fastq.10M_chunks0.gz TKO_ES159-SMF_MM_TKO_DE_R1.ERR4165150_2.fastq.10M_chunks0.gz
/oak/stanford/groups/akundaje/marinovg/programs/trim_galore_v0.4.4/trim_galore --path_to_cutadapt ~/anaconda2/bin/cutadapt --clip_R1 9 --clip_R2 9 --three_prime_clip_r1 6 --three_prime_clip_r2 6 --paired TKO_ES159-SMF_MM_TKO_DE_R1.ERR4165150_1.fastq.10M_chunks1.gz TKO_ES159-SMF_MM_TKO_DE_R1.ERR4165150_2.fastq.10M_chunks1.gz
/oak/stanford/groups/akundaje/marinovg/programs/trim_galore_v0.4.4/trim_galore --path_to_cutadapt ~/anaconda2/bin/cutadapt --clip_R1 9 --clip_R2 9 --three_prime_clip_r1 6 --three_prime_clip_r2 6 --paired TKO_ES159-SMF_MM_TKO_DE_R1.ERR4165150_1.fastq.10M_chunks2.gz TKO_ES159-SMF_MM_TKO_DE_R1.ERR4165150_2.fastq.10M_chunks2.gz
/oak/stanford/groups/akundaje/marinovg/programs/trim_galore_v0.4.4/trim_galore --path_to_cutadapt ~/anaconda2/bin/cutadapt --clip_R1 9 --clip_R2 9 --three_prime_clip_r1 6 --three_prime_clip_r2 6 --paired TKO_ES159-SMF_MM_TKO_DE_R1.ERR4165150_1.fastq.10M_chunks3.gz TKO_ES159-SMF_MM_TKO_DE_R1.ERR4165150_2.fastq.10M_chunks3.gz
/oak/stanford/groups/akundaje/marinovg/programs/trim_galore_v0.4.4/trim_galore --path_to_cutadapt ~/anaconda2/bin/cutadapt --clip_R1 9 --clip_R2 9 --three_prime_clip_r1 6 --three_prime_clip_r2 6 --paired TKO_ES159-SMF_MM_TKO_DE_R1.ERR4165152_1.fastq.10M_chunks0.gz TKO_ES159-SMF_MM_TKO_DE_R1.ERR4165152_2.fastq.10M_chunks0.gz
/oak/stanford/groups/akundaje/marinovg/programs/trim_galore_v0.4.4/trim_galore --path_to_cutadapt ~/anaconda2/bin/cutadapt --clip_R1 9 --clip_R2 9 --three_prime_clip_r1 6 --three_prime_clip_r2 6 --paired TKO_ES159-SMF_MM_TKO_DE_R1.ERR4165152_1.fastq.10M_chunks1.gz TKO_ES159-SMF_MM_TKO_DE_R1.ERR4165152_2.fastq.10M_chunks1.gz
/oak/stanford/groups/akundaje/marinovg/programs/trim_galore_v0.4.4/trim_galore --path_to_cutadapt ~/anaconda2/bin/cutadapt --clip_R1 9 --clip_R2 9 --three_prime_clip_r1 6 --three_prime_clip_r2 6 --paired TKO_ES159-SMF_MM_TKO_DE_R1.ERR4165152_1.fastq.10M_chunks2.gz TKO_ES159-SMF_MM_TKO_DE_R1.ERR4165152_2.fastq.10M_chunks2.gz
/oak/stanford/groups/akundaje/marinovg/programs/trim_galore_v0.4.4/trim_galore --path_to_cutadapt ~/anaconda2/bin/cutadapt --clip_R1 9 --clip_R2 9 --three_prime_clip_r1 6 --three_prime_clip_r2 6 --paired TKO_ES159-SMF_MM_TKO_DE_R1.ERR4165152_1.fastq.10M_chunks3.gz TKO_ES159-SMF_MM_TKO_DE_R1.ERR4165152_2.fastq.10M_chunks3.gz
/oak/stanford/groups/akundaje/marinovg/programs/trim_galore_v0.4.4/trim_galore --path_to_cutadapt ~/anaconda2/bin/cutadapt --clip_R1 9 --clip_R2 9 --three_prime_clip_r1 6 --three_prime_clip_r2 6 --paired TKO_ES159-SMF_MM_TKO_DE_R1.ERR4165154_1.fastq.10M_chunks0.gz TKO_ES159-SMF_MM_TKO_DE_R1.ERR4165154_2.fastq.10M_chunks0.gz
/oak/stanford/groups/akundaje/marinovg/programs/trim_galore_v0.4.4/trim_galore --path_to_cutadapt ~/anaconda2/bin/cutadapt --clip_R1 9 --clip_R2 9 --three_prime_clip_r1 6 --three_prime_clip_r2 6 --paired TKO_ES159-SMF_MM_TKO_DE_R1.ERR4165154_1.fastq.10M_chunks1.gz TKO_ES159-SMF_MM_TKO_DE_R1.ERR4165154_2.fastq.10M_chunks1.gz
/oak/stanford/groups/akundaje/marinovg/programs/trim_galore_v0.4.4/trim_galore --path_to_cutadapt ~/anaconda2/bin/cutadapt --clip_R1 9 --clip_R2 9 --three_prime_clip_r1 6 --three_prime_clip_r2 6 --paired TKO_ES159-SMF_MM_TKO_DE_R1.ERR4165154_1.fastq.10M_chunks10.gz TKO_ES159-SMF_MM_TKO_DE_R1.ERR4165154_2.fastq.10M_chunks10.gz
/oak/stanford/groups/akundaje/marinovg/programs/trim_galore_v0.4.4/trim_galore --path_to_cutadapt ~/anaconda2/bin/cutadapt --clip_R1 9 --clip_R2 9 --three_prime_clip_r1 6 --three_prime_clip_r2 6 --paired TKO_ES159-SMF_MM_TKO_DE_R1.ERR4165154_1.fastq.10M_chunks11.gz TKO_ES159-SMF_MM_TKO_DE_R1.ERR4165154_2.fastq.10M_chunks11.gz
/oak/stanford/groups/akundaje/marinovg/programs/trim_galore_v0.4.4/trim_galore --path_to_cutadapt ~/anaconda2/bin/cutadapt --clip_R1 9 --clip_R2 9 --three_prime_clip_r1 6 --three_prime_clip_r2 6 --paired TKO_ES159-SMF_MM_TKO_DE_R1.ERR4165154_1.fastq.10M_chunks12.gz TKO_ES159-SMF_MM_TKO_DE_R1.ERR4165154_2.fastq.10M_chunks12.gz
/oak/stanford/groups/akundaje/marinovg/programs/trim_galore_v0.4.4/trim_galore --path_to_cutadapt ~/anaconda2/bin/cutadapt --clip_R1 9 --clip_R2 9 --three_prime_clip_r1 6 --three_prime_clip_r2 6 --paired TKO_ES159-SMF_MM_TKO_DE_R1.ERR4165154_1.fastq.10M_chunks13.gz TKO_ES159-SMF_MM_TKO_DE_R1.ERR4165154_2.fastq.10M_chunks13.gz
/oak/stanford/groups/akundaje/marinovg/programs/trim_galore_v0.4.4/trim_galore --path_to_cutadapt ~/anaconda2/bin/cutadapt --clip_R1 9 --clip_R2 9 --three_prime_clip_r1 6 --three_prime_clip_r2 6 --paired TKO_ES159-SMF_MM_TKO_DE_R1.ERR4165154_1.fastq.10M_chunks14.gz TKO_ES159-SMF_MM_TKO_DE_R1.ERR4165154_2.fastq.10M_chunks14.gz
/oak/stanford/groups/akundaje/marinovg/programs/trim_galore_v0.4.4/trim_galore --path_to_cutadapt ~/anaconda2/bin/cutadapt --clip_R1 9 --clip_R2 9 --three_prime_clip_r1 6 --three_prime_clip_r2 6 --paired TKO_ES159-SMF_MM_TKO_DE_R1.ERR4165154_1.fastq.10M_chunks15.gz TKO_ES159-SMF_MM_TKO_DE_R1.ERR4165154_2.fastq.10M_chunks15.gz
/oak/stanford/groups/akundaje/marinovg/programs/trim_galore_v0.4.4/trim_galore --path_to_cutadapt ~/anaconda2/bin/cutadapt --clip_R1 9 --clip_R2 9 --three_prime_clip_r1 6 --three_prime_clip_r2 6 --paired TKO_ES159-SMF_MM_TKO_DE_R1.ERR4165154_1.fastq.10M_chunks16.gz TKO_ES159-SMF_MM_TKO_DE_R1.ERR4165154_2.fastq.10M_chunks16.gz
/oak/stanford/groups/akundaje/marinovg/programs/trim_galore_v0.4.4/trim_galore --path_to_cutadapt ~/anaconda2/bin/cutadapt --clip_R1 9 --clip_R2 9 --three_prime_clip_r1 6 --three_prime_clip_r2 6 --paired TKO_ES159-SMF_MM_TKO_DE_R1.ERR4165154_1.fastq.10M_chunks17.gz TKO_ES159-SMF_MM_TKO_DE_R1.ERR4165154_2.fastq.10M_chunks17.gz
/oak/stanford/groups/akundaje/marinovg/programs/trim_galore_v0.4.4/trim_galore --path_to_cutadapt ~/anaconda2/bin/cutadapt --clip_R1 9 --clip_R2 9 --three_prime_clip_r1 6 --three_prime_clip_r2 6 --paired TKO_ES159-SMF_MM_TKO_DE_R1.ERR4165154_1.fastq.10M_chunks18.gz TKO_ES159-SMF_MM_TKO_DE_R1.ERR4165154_2.fastq.10M_chunks18.gz
/oak/stanford/groups/akundaje/marinovg/programs/trim_galore_v0.4.4/trim_galore --path_to_cutadapt ~/anaconda2/bin/cutadapt --clip_R1 9 --clip_R2 9 --three_prime_clip_r1 6 --three_prime_clip_r2 6 --paired TKO_ES159-SMF_MM_TKO_DE_R1.ERR4165154_1.fastq.10M_chunks2.gz TKO_ES159-SMF_MM_TKO_DE_R1.ERR4165154_2.fastq.10M_chunks2.gz
/oak/stanford/groups/akundaje/marinovg/programs/trim_galore_v0.4.4/trim_galore --path_to_cutadapt ~/anaconda2/bin/cutadapt --clip_R1 9 --clip_R2 9 --three_prime_clip_r1 6 --three_prime_clip_r2 6 --paired TKO_ES159-SMF_MM_TKO_DE_R1.ERR4165154_1.fastq.10M_chunks3.gz TKO_ES159-SMF_MM_TKO_DE_R1.ERR4165154_2.fastq.10M_chunks3.gz
/oak/stanford/groups/akundaje/marinovg/programs/trim_galore_v0.4.4/trim_galore --path_to_cutadapt ~/anaconda2/bin/cutadapt --clip_R1 9 --clip_R2 9 --three_prime_clip_r1 6 --three_prime_clip_r2 6 --paired TKO_ES159-SMF_MM_TKO_DE_R1.ERR4165154_1.fastq.10M_chunks4.gz TKO_ES159-SMF_MM_TKO_DE_R1.ERR4165154_2.fastq.10M_chunks4.gz
/oak/stanford/groups/akundaje/marinovg/programs/trim_galore_v0.4.4/trim_galore --path_to_cutadapt ~/anaconda2/bin/cutadapt --clip_R1 9 --clip_R2 9 --three_prime_clip_r1 6 --three_prime_clip_r2 6 --paired TKO_ES159-SMF_MM_TKO_DE_R1.ERR4165154_1.fastq.10M_chunks5.gz TKO_ES159-SMF_MM_TKO_DE_R1.ERR4165154_2.fastq.10M_chunks5.gz
/oak/stanford/groups/akundaje/marinovg/programs/trim_galore_v0.4.4/trim_galore --path_to_cutadapt ~/anaconda2/bin/cutadapt --clip_R1 9 --clip_R2 9 --three_prime_clip_r1 6 --three_prime_clip_r2 6 --paired TKO_ES159-SMF_MM_TKO_DE_R1.ERR4165154_1.fastq.10M_chunks6.gz TKO_ES159-SMF_MM_TKO_DE_R1.ERR4165154_2.fastq.10M_chunks6.gz
/oak/stanford/groups/akundaje/marinovg/programs/trim_galore_v0.4.4/trim_galore --path_to_cutadapt ~/anaconda2/bin/cutadapt --clip_R1 9 --clip_R2 9 --three_prime_clip_r1 6 --three_prime_clip_r2 6 --paired TKO_ES159-SMF_MM_TKO_DE_R1.ERR4165154_1.fastq.10M_chunks7.gz TKO_ES159-SMF_MM_TKO_DE_R1.ERR4165154_2.fastq.10M_chunks7.gz
/oak/stanford/groups/akundaje/marinovg/programs/trim_galore_v0.4.4/trim_galore --path_to_cutadapt ~/anaconda2/bin/cutadapt --clip_R1 9 --clip_R2 9 --three_prime_clip_r1 6 --three_prime_clip_r2 6 --paired TKO_ES159-SMF_MM_TKO_DE_R1.ERR4165154_1.fastq.10M_chunks8.gz TKO_ES159-SMF_MM_TKO_DE_R1.ERR4165154_2.fastq.10M_chunks8.gz
/oak/stanford/groups/akundaje/marinovg/programs/trim_galore_v0.4.4/trim_galore --path_to_cutadapt ~/anaconda2/bin/cutadapt --clip_R1 9 --clip_R2 9 --three_prime_clip_r1 6 --three_prime_clip_r2 6 --paired TKO_ES159-SMF_MM_TKO_DE_R1.ERR4165154_1.fastq.10M_chunks9.gz TKO_ES159-SMF_MM_TKO_DE_R1.ERR4165154_2.fastq.10M_chunks9.gz
/oak/stanford/groups/akundaje/marinovg/programs/trim_galore_v0.4.4/trim_galore --path_to_cutadapt ~/anaconda2/bin/cutadapt --clip_R1 9 --clip_R2 9 --three_prime_clip_r1 6 --three_prime_clip_r2 6 --paired TKO_ES159-SMF_MM_TKO_DE_R2.ERR4165145_1.fastq.10M_chunks0.gz TKO_ES159-SMF_MM_TKO_DE_R2.ERR4165145_2.fastq.10M_chunks0.gz
/oak/stanford/groups/akundaje/marinovg/programs/trim_galore_v0.4.4/trim_galore --path_to_cutadapt ~/anaconda2/bin/cutadapt --clip_R1 9 --clip_R2 9 --three_prime_clip_r1 6 --three_prime_clip_r2 6 --paired TKO_ES159-SMF_MM_TKO_DE_R2.ERR4165145_1.fastq.10M_chunks1.gz TKO_ES159-SMF_MM_TKO_DE_R2.ERR4165145_2.fastq.10M_chunks1.gz
/oak/stanford/groups/akundaje/marinovg/programs/trim_galore_v0.4.4/trim_galore --path_to_cutadapt ~/anaconda2/bin/cutadapt --clip_R1 9 --clip_R2 9 --three_prime_clip_r1 6 --three_prime_clip_r2 6 --paired TKO_ES159-SMF_MM_TKO_DE_R2.ERR4165145_1.fastq.10M_chunks2.gz TKO_ES159-SMF_MM_TKO_DE_R2.ERR4165145_2.fastq.10M_chunks2.gz
/oak/stanford/groups/akundaje/marinovg/programs/trim_galore_v0.4.4/trim_galore --path_to_cutadapt ~/anaconda2/bin/cutadapt --clip_R1 9 --clip_R2 9 --three_prime_clip_r1 6 --three_prime_clip_r2 6 --paired TKO_ES159-SMF_MM_TKO_DE_R2.ERR4165145_1.fastq.10M_chunks3.gz TKO_ES159-SMF_MM_TKO_DE_R2.ERR4165145_2.fastq.10M_chunks3.gz
/oak/stanford/groups/akundaje/marinovg/programs/trim_galore_v0.4.4/trim_galore --path_to_cutadapt ~/anaconda2/bin/cutadapt --clip_R1 9 --clip_R2 9 --three_prime_clip_r1 6 --three_prime_clip_r2 6 --paired TKO_ES159-SMF_MM_TKO_DE_R2.ERR4165145_1.fastq.10M_chunks4.gz TKO_ES159-SMF_MM_TKO_DE_R2.ERR4165145_2.fastq.10M_chunks4.gz
/oak/stanford/groups/akundaje/marinovg/programs/trim_galore_v0.4.4/trim_galore --path_to_cutadapt ~/anaconda2/bin/cutadapt --clip_R1 9 --clip_R2 9 --three_prime_clip_r1 6 --three_prime_clip_r2 6 --paired TKO_ES159-SMF_MM_TKO_DE_R2.ERR4165145_1.fastq.10M_chunks5.gz TKO_ES159-SMF_MM_TKO_DE_R2.ERR4165145_2.fastq.10M_chunks5.gz
/oak/stanford/groups/akundaje/marinovg/programs/trim_galore_v0.4.4/trim_galore --path_to_cutadapt ~/anaconda2/bin/cutadapt --clip_R1 9 --clip_R2 9 --three_prime_clip_r1 6 --three_prime_clip_r2 6 --paired TKO_ES159-SMF_MM_TKO_DE_R2.ERR4165145_1.fastq.10M_chunks6.gz TKO_ES159-SMF_MM_TKO_DE_R2.ERR4165145_2.fastq.10M_chunks6.gz
/oak/stanford/groups/akundaje/marinovg/programs/trim_galore_v0.4.4/trim_galore --path_to_cutadapt ~/anaconda2/bin/cutadapt --clip_R1 9 --clip_R2 9 --three_prime_clip_r1 6 --three_prime_clip_r2 6 --paired TKO_ES159-SMF_MM_TKO_DE_R2.ERR4165145_1.fastq.10M_chunks7.gz TKO_ES159-SMF_MM_TKO_DE_R2.ERR4165145_2.fastq.10M_chunks7.gz
/oak/stanford/groups/akundaje/marinovg/programs/trim_galore_v0.4.4/trim_galore --path_to_cutadapt ~/anaconda2/bin/cutadapt --clip_R1 9 --clip_R2 9 --three_prime_clip_r1 6 --three_prime_clip_r2 6 --paired TKO_ES159-SMF_MM_TKO_DE_R2.ERR4165148_1.fastq.10M_chunks0.gz TKO_ES159-SMF_MM_TKO_DE_R2.ERR4165148_2.fastq.10M_chunks0.gz
/oak/stanford/groups/akundaje/marinovg/programs/trim_galore_v0.4.4/trim_galore --path_to_cutadapt ~/anaconda2/bin/cutadapt --clip_R1 9 --clip_R2 9 --three_prime_clip_r1 6 --three_prime_clip_r2 6 --paired TKO_ES159-SMF_MM_TKO_DE_R2.ERR4165148_1.fastq.10M_chunks1.gz TKO_ES159-SMF_MM_TKO_DE_R2.ERR4165148_2.fastq.10M_chunks1.gz
/oak/stanford/groups/akundaje/marinovg/programs/trim_galore_v0.4.4/trim_galore --path_to_cutadapt ~/anaconda2/bin/cutadapt --clip_R1 9 --clip_R2 9 --three_prime_clip_r1 6 --three_prime_clip_r2 6 --paired TKO_ES159-SMF_MM_TKO_DE_R2.ERR4165148_1.fastq.10M_chunks10.gz TKO_ES159-SMF_MM_TKO_DE_R2.ERR4165148_2.fastq.10M_chunks10.gz
/oak/stanford/groups/akundaje/marinovg/programs/trim_galore_v0.4.4/trim_galore --path_to_cutadapt ~/anaconda2/bin/cutadapt --clip_R1 9 --clip_R2 9 --three_prime_clip_r1 6 --three_prime_clip_r2 6 --paired TKO_ES159-SMF_MM_TKO_DE_R2.ERR4165148_1.fastq.10M_chunks11.gz TKO_ES159-SMF_MM_TKO_DE_R2.ERR4165148_2.fastq.10M_chunks11.gz
/oak/stanford/groups/akundaje/marinovg/programs/trim_galore_v0.4.4/trim_galore --path_to_cutadapt ~/anaconda2/bin/cutadapt --clip_R1 9 --clip_R2 9 --three_prime_clip_r1 6 --three_prime_clip_r2 6 --paired TKO_ES159-SMF_MM_TKO_DE_R2.ERR4165148_1.fastq.10M_chunks12.gz TKO_ES159-SMF_MM_TKO_DE_R2.ERR4165148_2.fastq.10M_chunks12.gz
/oak/stanford/groups/akundaje/marinovg/programs/trim_galore_v0.4.4/trim_galore --path_to_cutadapt ~/anaconda2/bin/cutadapt --clip_R1 9 --clip_R2 9 --three_prime_clip_r1 6 --three_prime_clip_r2 6 --paired TKO_ES159-SMF_MM_TKO_DE_R2.ERR4165148_1.fastq.10M_chunks13.gz TKO_ES159-SMF_MM_TKO_DE_R2.ERR4165148_2.fastq.10M_chunks13.gz
/oak/stanford/groups/akundaje/marinovg/programs/trim_galore_v0.4.4/trim_galore --path_to_cutadapt ~/anaconda2/bin/cutadapt --clip_R1 9 --clip_R2 9 --three_prime_clip_r1 6 --three_prime_clip_r2 6 --paired TKO_ES159-SMF_MM_TKO_DE_R2.ERR4165148_1.fastq.10M_chunks14.gz TKO_ES159-SMF_MM_TKO_DE_R2.ERR4165148_2.fastq.10M_chunks14.gz
/oak/stanford/groups/akundaje/marinovg/programs/trim_galore_v0.4.4/trim_galore --path_to_cutadapt ~/anaconda2/bin/cutadapt --clip_R1 9 --clip_R2 9 --three_prime_clip_r1 6 --three_prime_clip_r2 6 --paired TKO_ES159-SMF_MM_TKO_DE_R2.ERR4165148_1.fastq.10M_chunks2.gz TKO_ES159-SMF_MM_TKO_DE_R2.ERR4165148_2.fastq.10M_chunks2.gz
/oak/stanford/groups/akundaje/marinovg/programs/trim_galore_v0.4.4/trim_galore --path_to_cutadapt ~/anaconda2/bin/cutadapt --clip_R1 9 --clip_R2 9 --three_prime_clip_r1 6 --three_prime_clip_r2 6 --paired TKO_ES159-SMF_MM_TKO_DE_R2.ERR4165148_1.fastq.10M_chunks3.gz TKO_ES159-SMF_MM_TKO_DE_R2.ERR4165148_2.fastq.10M_chunks3.gz
/oak/stanford/groups/akundaje/marinovg/programs/trim_galore_v0.4.4/trim_galore --path_to_cutadapt ~/anaconda2/bin/cutadapt --clip_R1 9 --clip_R2 9 --three_prime_clip_r1 6 --three_prime_clip_r2 6 --paired TKO_ES159-SMF_MM_TKO_DE_R2.ERR4165148_1.fastq.10M_chunks4.gz TKO_ES159-SMF_MM_TKO_DE_R2.ERR4165148_2.fastq.10M_chunks4.gz
/oak/stanford/groups/akundaje/marinovg/programs/trim_galore_v0.4.4/trim_galore --path_to_cutadapt ~/anaconda2/bin/cutadapt --clip_R1 9 --clip_R2 9 --three_prime_clip_r1 6 --three_prime_clip_r2 6 --paired TKO_ES159-SMF_MM_TKO_DE_R2.ERR4165148_1.fastq.10M_chunks5.gz TKO_ES159-SMF_MM_TKO_DE_R2.ERR4165148_2.fastq.10M_chunks5.gz
/oak/stanford/groups/akundaje/marinovg/programs/trim_galore_v0.4.4/trim_galore --path_to_cutadapt ~/anaconda2/bin/cutadapt --clip_R1 9 --clip_R2 9 --three_prime_clip_r1 6 --three_prime_clip_r2 6 --paired TKO_ES159-SMF_MM_TKO_DE_R2.ERR4165148_1.fastq.10M_chunks6.gz TKO_ES159-SMF_MM_TKO_DE_R2.ERR4165148_2.fastq.10M_chunks6.gz
/oak/stanford/groups/akundaje/marinovg/programs/trim_galore_v0.4.4/trim_galore --path_to_cutadapt ~/anaconda2/bin/cutadapt --clip_R1 9 --clip_R2 9 --three_prime_clip_r1 6 --three_prime_clip_r2 6 --paired TKO_ES159-SMF_MM_TKO_DE_R2.ERR4165148_1.fastq.10M_chunks7.gz TKO_ES159-SMF_MM_TKO_DE_R2.ERR4165148_2.fastq.10M_chunks7.gz
/oak/stanford/groups/akundaje/marinovg/programs/trim_galore_v0.4.4/trim_galore --path_to_cutadapt ~/anaconda2/bin/cutadapt --clip_R1 9 --clip_R2 9 --three_prime_clip_r1 6 --three_prime_clip_r2 6 --paired TKO_ES159-SMF_MM_TKO_DE_R2.ERR4165148_1.fastq.10M_chunks8.gz TKO_ES159-SMF_MM_TKO_DE_R2.ERR4165148_2.fastq.10M_chunks8.gz
/oak/stanford/groups/akundaje/marinovg/programs/trim_galore_v0.4.4/trim_galore --path_to_cutadapt ~/anaconda2/bin/cutadapt --clip_R1 9 --clip_R2 9 --three_prime_clip_r1 6 --three_prime_clip_r2 6 --paired TKO_ES159-SMF_MM_TKO_DE_R2.ERR4165148_1.fastq.10M_chunks9.gz TKO_ES159-SMF_MM_TKO_DE_R2.ERR4165148_2.fastq.10M_chunks9.gz
/oak/stanford/groups/akundaje/marinovg/programs/trim_galore_v0.4.4/trim_galore --path_to_cutadapt ~/anaconda2/bin/cutadapt --clip_R1 9 --clip_R2 9 --three_prime_clip_r1 6 --three_prime_clip_r2 6 --paired TKO_ES159-SMF_MM_TKO_DE_R2.ERR4165149_1.fastq.10M_chunks0.gz TKO_ES159-SMF_MM_TKO_DE_R2.ERR4165149_2.fastq.10M_chunks0.gz
/oak/stanford/groups/akundaje/marinovg/programs/trim_galore_v0.4.4/trim_galore --path_to_cutadapt ~/anaconda2/bin/cutadapt --clip_R1 9 --clip_R2 9 --three_prime_clip_r1 6 --three_prime_clip_r2 6 --paired TKO_ES159-SMF_MM_TKO_DE_R2.ERR4165149_1.fastq.10M_chunks1.gz TKO_ES159-SMF_MM_TKO_DE_R2.ERR4165149_2.fastq.10M_chunks1.gz
/oak/stanford/groups/akundaje/marinovg/programs/trim_galore_v0.4.4/trim_galore --path_to_cutadapt ~/anaconda2/bin/cutadapt --clip_R1 9 --clip_R2 9 --three_prime_clip_r1 6 --three_prime_clip_r2 6 --paired TKO_ES159-SMF_MM_TKO_DE_R2.ERR4165149_1.fastq.10M_chunks2.gz TKO_ES159-SMF_MM_TKO_DE_R2.ERR4165149_2.fastq.10M_chunks2.gz
/oak/stanford/groups/akundaje/marinovg/programs/trim_galore_v0.4.4/trim_galore --path_to_cutadapt ~/anaconda2/bin/cutadapt --clip_R1 9 --clip_R2 9 --three_prime_clip_r1 6 --three_prime_clip_r2 6 --paired TKO_ES159-SMF_MM_TKO_DE_R2.ERR4165149_1.fastq.10M_chunks3.gz TKO_ES159-SMF_MM_TKO_DE_R2.ERR4165149_2.fastq.10M_chunks3.gz
/oak/stanford/groups/akundaje/marinovg/programs/trim_galore_v0.4.4/trim_galore --path_to_cutadapt ~/anaconda2/bin/cutadapt --clip_R1 9 --clip_R2 9 --three_prime_clip_r1 6 --three_prime_clip_r2 6 --paired TKO_ES159-SMF_MM_TKO_DE_R2.ERR4165149_1.fastq.10M_chunks4.gz TKO_ES159-SMF_MM_TKO_DE_R2.ERR4165149_2.fastq.10M_chunks4.gz
/oak/stanford/groups/akundaje/marinovg/programs/trim_galore_v0.4.4/trim_galore --path_to_cutadapt ~/anaconda2/bin/cutadapt --clip_R1 9 --clip_R2 9 --three_prime_clip_r1 6 --three_prime_clip_r2 6 --paired TKO_ES159-SMF_MM_TKO_DE_R2.ERR4165149_1.fastq.10M_chunks5.gz TKO_ES159-SMF_MM_TKO_DE_R2.ERR4165149_2.fastq.10M_chunks5.gz
/oak/stanford/groups/akundaje/marinovg/programs/trim_galore_v0.4.4/trim_galore --path_to_cutadapt ~/anaconda2/bin/cutadapt --clip_R1 9 --clip_R2 9 --three_prime_clip_r1 6 --three_prime_clip_r2 6 --paired TKO_ES159-SMF_MM_TKO_DE_R2.ERR4165149_1.fastq.10M_chunks6.gz TKO_ES159-SMF_MM_TKO_DE_R2.ERR4165149_2.fastq.10M_chunks6.gz
/oak/stanford/groups/akundaje/marinovg/programs/trim_galore_v0.4.4/trim_galore --path_to_cutadapt ~/anaconda2/bin/cutadapt --clip_R1 9 --clip_R2 9 --three_prime_clip_r1 6 --three_prime_clip_r2 6 --paired TKO_ES159-SMF_MM_TKO_DE_R2.ERR4165149_1.fastq.10M_chunks7.gz TKO_ES159-SMF_MM_TKO_DE_R2.ERR4165149_2.fastq.10M_chunks7.gz
/oak/stanford/groups/akundaje/marinovg/programs/trim_galore_v0.4.4/trim_galore --path_to_cutadapt ~/anaconda2/bin/cutadapt --clip_R1 9 --clip_R2 9 --three_prime_clip_r1 6 --three_prime_clip_r2 6 --paired TKO_NRF1KD_DE_P1_R1.ERR4078781_1.fastq.10M_chunks0.gz TKO_NRF1KD_DE_P1_R1.ERR4078781_2.fastq.10M_chunks0.gz
/oak/stanford/groups/akundaje/marinovg/programs/trim_galore_v0.4.4/trim_galore --path_to_cutadapt ~/anaconda2/bin/cutadapt --clip_R1 9 --clip_R2 9 --three_prime_clip_r1 6 --three_prime_clip_r2 6 --paired TKO_NRF1KD_DE_P1_R2.ERR4078801_1.fastq.10M_chunks0.gz TKO_NRF1KD_DE_P1_R2.ERR4078801_2.fastq.10M_chunks0.gz
/oak/stanford/groups/akundaje/marinovg/programs/trim_galore_v0.4.4/trim_galore --path_to_cutadapt ~/anaconda2/bin/cutadapt --clip_R1 9 --clip_R2 9 --three_prime_clip_r1 6 --three_prime_clip_r2 6 --paired TKO_NRF1KD_DE_P2_R1.ERR4078778_1.fastq.10M_chunks0.gz TKO_NRF1KD_DE_P2_R1.ERR4078778_2.fastq.10M_chunks0.gz
/oak/stanford/groups/akundaje/marinovg/programs/trim_galore_v0.4.4/trim_galore --path_to_cutadapt ~/anaconda2/bin/cutadapt --clip_R1 9 --clip_R2 9 --three_prime_clip_r1 6 --three_prime_clip_r2 6 --paired TKO_NRF1KD_DE_P2_R2.ERR4078782_1.fastq.10M_chunks0.gz TKO_NRF1KD_DE_P2_R2.ERR4078782_2.fastq.10M_chunks0.gz
/oak/stanford/groups/akundaje/marinovg/programs/trim_galore_v0.4.4/trim_galore --path_to_cutadapt ~/anaconda2/bin/cutadapt --clip_R1 9 --clip_R2 9 --three_prime_clip_r1 6 --three_prime_clip_r2 6 --paired TKO_NRF1KD_DE_P3_R1.ERR4078803_1.fastq.10M_chunks0.gz TKO_NRF1KD_DE_P3_R1.ERR4078803_2.fastq.10M_chunks0.gz
/oak/stanford/groups/akundaje/marinovg/programs/trim_galore_v0.4.4/trim_galore --path_to_cutadapt ~/anaconda2/bin/cutadapt --clip_R1 9 --clip_R2 9 --three_prime_clip_r1 6 --three_prime_clip_r2 6 --paired TKO_NRF1KD_DE_P3_R2.ERR4078788_1.fastq.10M_chunks0.gz TKO_NRF1KD_DE_P3_R2.ERR4078788_2.fastq.10M_chunks0.gz
/oak/stanford/groups/akundaje/marinovg/programs/trim_galore_v0.4.4/trim_galore --path_to_cutadapt ~/anaconda2/bin/cutadapt --clip_R1 9 --clip_R2 9 --three_prime_clip_r1 6 --three_prime_clip_r2 6 --paired TKO_Scramble_DE_P1_R1.ERR4078802_1.fastq.10M_chunks0.gz TKO_Scramble_DE_P1_R1.ERR4078802_2.fastq.10M_chunks0.gz
/oak/stanford/groups/akundaje/marinovg/programs/trim_galore_v0.4.4/trim_galore --path_to_cutadapt ~/anaconda2/bin/cutadapt --clip_R1 9 --clip_R2 9 --three_prime_clip_r1 6 --three_prime_clip_r2 6 --paired TKO_Scramble_DE_P1_R2.ERR4078794_1.fastq.10M_chunks0.gz TKO_Scramble_DE_P1_R2.ERR4078794_2.fastq.10M_chunks0.gz
/oak/stanford/groups/akundaje/marinovg/programs/trim_galore_v0.4.4/trim_galore --path_to_cutadapt ~/anaconda2/bin/cutadapt --clip_R1 9 --clip_R2 9 --three_prime_clip_r1 6 --three_prime_clip_r2 6 --paired TKO_Scramble_DE_P2_R1.ERR4078797_1.fastq.10M_chunks0.gz TKO_Scramble_DE_P2_R1.ERR4078797_2.fastq.10M_chunks0.gz
/oak/stanford/groups/akundaje/marinovg/programs/trim_galore_v0.4.4/trim_galore --path_to_cutadapt ~/anaconda2/bin/cutadapt --clip_R1 9 --clip_R2 9 --three_prime_clip_r1 6 --three_prime_clip_r2 6 --paired TKO_Scramble_DE_P2_R2.ERR4078796_1.fastq.10M_chunks0.gz TKO_Scramble_DE_P2_R2.ERR4078796_2.fastq.10M_chunks0.gz
/oak/stanford/groups/akundaje/marinovg/programs/trim_galore_v0.4.4/trim_galore --path_to_cutadapt ~/anaconda2/bin/cutadapt --clip_R1 9 --clip_R2 9 --three_prime_clip_r1 6 --three_prime_clip_r2 6 --paired TKO_Scramble_DE_P3_R1.ERR4078779_1.fastq.10M_chunks0.gz TKO_Scramble_DE_P3_R1.ERR4078779_2.fastq.10M_chunks0.gz
/oak/stanford/groups/akundaje/marinovg/programs/trim_galore_v0.4.4/trim_galore --path_to_cutadapt ~/anaconda2/bin/cutadapt --clip_R1 9 --clip_R2 9 --three_prime_clip_r1 6 --three_prime_clip_r2 6 --paired TKO_Scramble_DE_P3_R2.ERR4078789_1.fastq.10M_chunks0.gz TKO_Scramble_DE_P3_R2.ERR4078789_2.fastq.10M_chunks0.gz
/oak/stanford/groups/akundaje/marinovg/programs/trim_galore_v0.4.4/trim_galore --path_to_cutadapt ~/anaconda2/bin/cutadapt --clip_R1 9 --clip_R2 9 --three_prime_clip_r1 6 --three_prime_clip_r2 6 --paired TKO_Xlink_DE_P1_R1.ERR4078799_1.fastq.10M_chunks0.gz TKO_Xlink_DE_P1_R1.ERR4078799_2.fastq.10M_chunks0.gz
/oak/stanford/groups/akundaje/marinovg/programs/trim_galore_v0.4.4/trim_galore --path_to_cutadapt ~/anaconda2/bin/cutadapt --clip_R1 9 --clip_R2 9 --three_prime_clip_r1 6 --three_prime_clip_r2 6 --paired TKO_Xlink_DE_P1_R2.ERR4078786_1.fastq.10M_chunks0.gz TKO_Xlink_DE_P1_R2.ERR4078786_2.fastq.10M_chunks0.gz
/oak/stanford/groups/akundaje/marinovg/programs/trim_galore_v0.4.4/trim_galore --path_to_cutadapt ~/anaconda2/bin/cutadapt --clip_R1 9 --clip_R2 9 --three_prime_clip_r1 6 --three_prime_clip_r2 6 --paired TKO_Xlink_DE_P2_R1.ERR4078795_1.fastq.10M_chunks0.gz TKO_Xlink_DE_P2_R1.ERR4078795_2.fastq.10M_chunks0.gz
/oak/stanford/groups/akundaje/marinovg/programs/trim_galore_v0.4.4/trim_galore --path_to_cutadapt ~/anaconda2/bin/cutadapt --clip_R1 9 --clip_R2 9 --three_prime_clip_r1 6 --three_prime_clip_r2 6 --paired TKO_Xlink_DE_P2_R2.ERR4078780_1.fastq.10M_chunks0.gz TKO_Xlink_DE_P2_R2.ERR4078780_2.fastq.10M_chunks0.gz