python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py zzUndetermined_S0_L001_R1_001.fastq.gz0 zzUndetermined_S0_L001_R1_001.fastq.gz0 | python /oak/stanford/groups/akundaje/marinovg/code/demultiplexFASTQDualIndex.py - SampleSheet-nonSHARE-seq.config 1 -prefix zz -suffix -L001-0
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py zzUndetermined_S0_L001_R1_001.fastq.gz1 zzUndetermined_S0_L001_R1_001.fastq.gz1 | python /oak/stanford/groups/akundaje/marinovg/code/demultiplexFASTQDualIndex.py - SampleSheet-nonSHARE-seq.config 1 -prefix zz -suffix -L001-1
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py zzUndetermined_S0_L001_R1_001.fastq.gz10 zzUndetermined_S0_L001_R1_001.fastq.gz10 | python /oak/stanford/groups/akundaje/marinovg/code/demultiplexFASTQDualIndex.py - SampleSheet-nonSHARE-seq.config 1 -prefix zz -suffix -L001-10
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py zzUndetermined_S0_L001_R1_001.fastq.gz100 zzUndetermined_S0_L001_R1_001.fastq.gz100 | python /oak/stanford/groups/akundaje/marinovg/code/demultiplexFASTQDualIndex.py - SampleSheet-nonSHARE-seq.config 1 -prefix zz -suffix -L001-100
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py zzUndetermined_S0_L001_R1_001.fastq.gz101 zzUndetermined_S0_L001_R1_001.fastq.gz101 | python /oak/stanford/groups/akundaje/marinovg/code/demultiplexFASTQDualIndex.py - SampleSheet-nonSHARE-seq.config 1 -prefix zz -suffix -L001-101
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py zzUndetermined_S0_L001_R1_001.fastq.gz102 zzUndetermined_S0_L001_R1_001.fastq.gz102 | python /oak/stanford/groups/akundaje/marinovg/code/demultiplexFASTQDualIndex.py - SampleSheet-nonSHARE-seq.config 1 -prefix zz -suffix -L001-102
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py zzUndetermined_S0_L001_R1_001.fastq.gz103 zzUndetermined_S0_L001_R1_001.fastq.gz103 | python /oak/stanford/groups/akundaje/marinovg/code/demultiplexFASTQDualIndex.py - SampleSheet-nonSHARE-seq.config 1 -prefix zz -suffix -L001-103
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py zzUndetermined_S0_L001_R1_001.fastq.gz104 zzUndetermined_S0_L001_R1_001.fastq.gz104 | python /oak/stanford/groups/akundaje/marinovg/code/demultiplexFASTQDualIndex.py - SampleSheet-nonSHARE-seq.config 1 -prefix zz -suffix -L001-104
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py zzUndetermined_S0_L001_R1_001.fastq.gz105 zzUndetermined_S0_L001_R1_001.fastq.gz105 | python /oak/stanford/groups/akundaje/marinovg/code/demultiplexFASTQDualIndex.py - SampleSheet-nonSHARE-seq.config 1 -prefix zz -suffix -L001-105
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py zzUndetermined_S0_L001_R1_001.fastq.gz106 zzUndetermined_S0_L001_R1_001.fastq.gz106 | python /oak/stanford/groups/akundaje/marinovg/code/demultiplexFASTQDualIndex.py - SampleSheet-nonSHARE-seq.config 1 -prefix zz -suffix -L001-106
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py zzUndetermined_S0_L001_R1_001.fastq.gz107 zzUndetermined_S0_L001_R1_001.fastq.gz107 | python /oak/stanford/groups/akundaje/marinovg/code/demultiplexFASTQDualIndex.py - SampleSheet-nonSHARE-seq.config 1 -prefix zz -suffix -L001-107
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py zzUndetermined_S0_L001_R1_001.fastq.gz108 zzUndetermined_S0_L001_R1_001.fastq.gz108 | python /oak/stanford/groups/akundaje/marinovg/code/demultiplexFASTQDualIndex.py - SampleSheet-nonSHARE-seq.config 1 -prefix zz -suffix -L001-108
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py zzUndetermined_S0_L001_R1_001.fastq.gz109 zzUndetermined_S0_L001_R1_001.fastq.gz109 | python /oak/stanford/groups/akundaje/marinovg/code/demultiplexFASTQDualIndex.py - SampleSheet-nonSHARE-seq.config 1 -prefix zz -suffix -L001-109
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py zzUndetermined_S0_L001_R1_001.fastq.gz11 zzUndetermined_S0_L001_R1_001.fastq.gz11 | python /oak/stanford/groups/akundaje/marinovg/code/demultiplexFASTQDualIndex.py - SampleSheet-nonSHARE-seq.config 1 -prefix zz -suffix -L001-11
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py zzUndetermined_S0_L001_R1_001.fastq.gz110 zzUndetermined_S0_L001_R1_001.fastq.gz110 | python /oak/stanford/groups/akundaje/marinovg/code/demultiplexFASTQDualIndex.py - SampleSheet-nonSHARE-seq.config 1 -prefix zz -suffix -L001-110
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py zzUndetermined_S0_L001_R1_001.fastq.gz111 zzUndetermined_S0_L001_R1_001.fastq.gz111 | python /oak/stanford/groups/akundaje/marinovg/code/demultiplexFASTQDualIndex.py - SampleSheet-nonSHARE-seq.config 1 -prefix zz -suffix -L001-111
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py zzUndetermined_S0_L001_R1_001.fastq.gz112 zzUndetermined_S0_L001_R1_001.fastq.gz112 | python /oak/stanford/groups/akundaje/marinovg/code/demultiplexFASTQDualIndex.py - SampleSheet-nonSHARE-seq.config 1 -prefix zz -suffix -L001-112
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py zzUndetermined_S0_L001_R1_001.fastq.gz113 zzUndetermined_S0_L001_R1_001.fastq.gz113 | python /oak/stanford/groups/akundaje/marinovg/code/demultiplexFASTQDualIndex.py - SampleSheet-nonSHARE-seq.config 1 -prefix zz -suffix -L001-113
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py zzUndetermined_S0_L001_R1_001.fastq.gz114 zzUndetermined_S0_L001_R1_001.fastq.gz114 | python /oak/stanford/groups/akundaje/marinovg/code/demultiplexFASTQDualIndex.py - SampleSheet-nonSHARE-seq.config 1 -prefix zz -suffix -L001-114
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py zzUndetermined_S0_L001_R1_001.fastq.gz115 zzUndetermined_S0_L001_R1_001.fastq.gz115 | python /oak/stanford/groups/akundaje/marinovg/code/demultiplexFASTQDualIndex.py - SampleSheet-nonSHARE-seq.config 1 -prefix zz -suffix -L001-115
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py zzUndetermined_S0_L001_R1_001.fastq.gz116 zzUndetermined_S0_L001_R1_001.fastq.gz116 | python /oak/stanford/groups/akundaje/marinovg/code/demultiplexFASTQDualIndex.py - SampleSheet-nonSHARE-seq.config 1 -prefix zz -suffix -L001-116
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py zzUndetermined_S0_L001_R1_001.fastq.gz117 zzUndetermined_S0_L001_R1_001.fastq.gz117 | python /oak/stanford/groups/akundaje/marinovg/code/demultiplexFASTQDualIndex.py - SampleSheet-nonSHARE-seq.config 1 -prefix zz -suffix -L001-117
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py zzUndetermined_S0_L001_R1_001.fastq.gz118 zzUndetermined_S0_L001_R1_001.fastq.gz118 | python /oak/stanford/groups/akundaje/marinovg/code/demultiplexFASTQDualIndex.py - SampleSheet-nonSHARE-seq.config 1 -prefix zz -suffix -L001-118
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py zzUndetermined_S0_L001_R1_001.fastq.gz119 zzUndetermined_S0_L001_R1_001.fastq.gz119 | python /oak/stanford/groups/akundaje/marinovg/code/demultiplexFASTQDualIndex.py - SampleSheet-nonSHARE-seq.config 1 -prefix zz -suffix -L001-119
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py zzUndetermined_S0_L001_R1_001.fastq.gz12 zzUndetermined_S0_L001_R1_001.fastq.gz12 | python /oak/stanford/groups/akundaje/marinovg/code/demultiplexFASTQDualIndex.py - SampleSheet-nonSHARE-seq.config 1 -prefix zz -suffix -L001-12
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py zzUndetermined_S0_L001_R1_001.fastq.gz120 zzUndetermined_S0_L001_R1_001.fastq.gz120 | python /oak/stanford/groups/akundaje/marinovg/code/demultiplexFASTQDualIndex.py - SampleSheet-nonSHARE-seq.config 1 -prefix zz -suffix -L001-120
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py zzUndetermined_S0_L001_R1_001.fastq.gz121 zzUndetermined_S0_L001_R1_001.fastq.gz121 | python /oak/stanford/groups/akundaje/marinovg/code/demultiplexFASTQDualIndex.py - SampleSheet-nonSHARE-seq.config 1 -prefix zz -suffix -L001-121
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py zzUndetermined_S0_L001_R1_001.fastq.gz122 zzUndetermined_S0_L001_R1_001.fastq.gz122 | python /oak/stanford/groups/akundaje/marinovg/code/demultiplexFASTQDualIndex.py - SampleSheet-nonSHARE-seq.config 1 -prefix zz -suffix -L001-122
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py zzUndetermined_S0_L001_R1_001.fastq.gz123 zzUndetermined_S0_L001_R1_001.fastq.gz123 | python /oak/stanford/groups/akundaje/marinovg/code/demultiplexFASTQDualIndex.py - SampleSheet-nonSHARE-seq.config 1 -prefix zz -suffix -L001-123
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py zzUndetermined_S0_L001_R1_001.fastq.gz124 zzUndetermined_S0_L001_R1_001.fastq.gz124 | python /oak/stanford/groups/akundaje/marinovg/code/demultiplexFASTQDualIndex.py - SampleSheet-nonSHARE-seq.config 1 -prefix zz -suffix -L001-124
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py zzUndetermined_S0_L001_R1_001.fastq.gz125 zzUndetermined_S0_L001_R1_001.fastq.gz125 | python /oak/stanford/groups/akundaje/marinovg/code/demultiplexFASTQDualIndex.py - SampleSheet-nonSHARE-seq.config 1 -prefix zz -suffix -L001-125
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py zzUndetermined_S0_L001_R1_001.fastq.gz126 zzUndetermined_S0_L001_R1_001.fastq.gz126 | python /oak/stanford/groups/akundaje/marinovg/code/demultiplexFASTQDualIndex.py - SampleSheet-nonSHARE-seq.config 1 -prefix zz -suffix -L001-126
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py zzUndetermined_S0_L001_R1_001.fastq.gz127 zzUndetermined_S0_L001_R1_001.fastq.gz127 | python /oak/stanford/groups/akundaje/marinovg/code/demultiplexFASTQDualIndex.py - SampleSheet-nonSHARE-seq.config 1 -prefix zz -suffix -L001-127
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py zzUndetermined_S0_L001_R1_001.fastq.gz128 zzUndetermined_S0_L001_R1_001.fastq.gz128 | python /oak/stanford/groups/akundaje/marinovg/code/demultiplexFASTQDualIndex.py - SampleSheet-nonSHARE-seq.config 1 -prefix zz -suffix -L001-128
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py zzUndetermined_S0_L001_R1_001.fastq.gz129 zzUndetermined_S0_L001_R1_001.fastq.gz129 | python /oak/stanford/groups/akundaje/marinovg/code/demultiplexFASTQDualIndex.py - SampleSheet-nonSHARE-seq.config 1 -prefix zz -suffix -L001-129
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py zzUndetermined_S0_L001_R1_001.fastq.gz13 zzUndetermined_S0_L001_R1_001.fastq.gz13 | python /oak/stanford/groups/akundaje/marinovg/code/demultiplexFASTQDualIndex.py - SampleSheet-nonSHARE-seq.config 1 -prefix zz -suffix -L001-13
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py zzUndetermined_S0_L001_R1_001.fastq.gz14 zzUndetermined_S0_L001_R1_001.fastq.gz14 | python /oak/stanford/groups/akundaje/marinovg/code/demultiplexFASTQDualIndex.py - SampleSheet-nonSHARE-seq.config 1 -prefix zz -suffix -L001-14
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py zzUndetermined_S0_L001_R1_001.fastq.gz15 zzUndetermined_S0_L001_R1_001.fastq.gz15 | python /oak/stanford/groups/akundaje/marinovg/code/demultiplexFASTQDualIndex.py - SampleSheet-nonSHARE-seq.config 1 -prefix zz -suffix -L001-15
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py zzUndetermined_S0_L001_R1_001.fastq.gz16 zzUndetermined_S0_L001_R1_001.fastq.gz16 | python /oak/stanford/groups/akundaje/marinovg/code/demultiplexFASTQDualIndex.py - SampleSheet-nonSHARE-seq.config 1 -prefix zz -suffix -L001-16
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py zzUndetermined_S0_L001_R1_001.fastq.gz17 zzUndetermined_S0_L001_R1_001.fastq.gz17 | python /oak/stanford/groups/akundaje/marinovg/code/demultiplexFASTQDualIndex.py - SampleSheet-nonSHARE-seq.config 1 -prefix zz -suffix -L001-17
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py zzUndetermined_S0_L001_R1_001.fastq.gz18 zzUndetermined_S0_L001_R1_001.fastq.gz18 | python /oak/stanford/groups/akundaje/marinovg/code/demultiplexFASTQDualIndex.py - SampleSheet-nonSHARE-seq.config 1 -prefix zz -suffix -L001-18
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py zzUndetermined_S0_L001_R1_001.fastq.gz19 zzUndetermined_S0_L001_R1_001.fastq.gz19 | python /oak/stanford/groups/akundaje/marinovg/code/demultiplexFASTQDualIndex.py - SampleSheet-nonSHARE-seq.config 1 -prefix zz -suffix -L001-19
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py zzUndetermined_S0_L001_R1_001.fastq.gz2 zzUndetermined_S0_L001_R1_001.fastq.gz2 | python /oak/stanford/groups/akundaje/marinovg/code/demultiplexFASTQDualIndex.py - SampleSheet-nonSHARE-seq.config 1 -prefix zz -suffix -L001-2
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py zzUndetermined_S0_L001_R1_001.fastq.gz20 zzUndetermined_S0_L001_R1_001.fastq.gz20 | python /oak/stanford/groups/akundaje/marinovg/code/demultiplexFASTQDualIndex.py - SampleSheet-nonSHARE-seq.config 1 -prefix zz -suffix -L001-20
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py zzUndetermined_S0_L001_R1_001.fastq.gz21 zzUndetermined_S0_L001_R1_001.fastq.gz21 | python /oak/stanford/groups/akundaje/marinovg/code/demultiplexFASTQDualIndex.py - SampleSheet-nonSHARE-seq.config 1 -prefix zz -suffix -L001-21
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py zzUndetermined_S0_L001_R1_001.fastq.gz22 zzUndetermined_S0_L001_R1_001.fastq.gz22 | python /oak/stanford/groups/akundaje/marinovg/code/demultiplexFASTQDualIndex.py - SampleSheet-nonSHARE-seq.config 1 -prefix zz -suffix -L001-22
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py zzUndetermined_S0_L001_R1_001.fastq.gz23 zzUndetermined_S0_L001_R1_001.fastq.gz23 | python /oak/stanford/groups/akundaje/marinovg/code/demultiplexFASTQDualIndex.py - SampleSheet-nonSHARE-seq.config 1 -prefix zz -suffix -L001-23
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py zzUndetermined_S0_L001_R1_001.fastq.gz24 zzUndetermined_S0_L001_R1_001.fastq.gz24 | python /oak/stanford/groups/akundaje/marinovg/code/demultiplexFASTQDualIndex.py - SampleSheet-nonSHARE-seq.config 1 -prefix zz -suffix -L001-24
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py zzUndetermined_S0_L001_R1_001.fastq.gz25 zzUndetermined_S0_L001_R1_001.fastq.gz25 | python /oak/stanford/groups/akundaje/marinovg/code/demultiplexFASTQDualIndex.py - SampleSheet-nonSHARE-seq.config 1 -prefix zz -suffix -L001-25
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py zzUndetermined_S0_L001_R1_001.fastq.gz26 zzUndetermined_S0_L001_R1_001.fastq.gz26 | python /oak/stanford/groups/akundaje/marinovg/code/demultiplexFASTQDualIndex.py - SampleSheet-nonSHARE-seq.config 1 -prefix zz -suffix -L001-26
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py zzUndetermined_S0_L001_R1_001.fastq.gz27 zzUndetermined_S0_L001_R1_001.fastq.gz27 | python /oak/stanford/groups/akundaje/marinovg/code/demultiplexFASTQDualIndex.py - SampleSheet-nonSHARE-seq.config 1 -prefix zz -suffix -L001-27
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py zzUndetermined_S0_L001_R1_001.fastq.gz28 zzUndetermined_S0_L001_R1_001.fastq.gz28 | python /oak/stanford/groups/akundaje/marinovg/code/demultiplexFASTQDualIndex.py - SampleSheet-nonSHARE-seq.config 1 -prefix zz -suffix -L001-28
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py zzUndetermined_S0_L001_R1_001.fastq.gz29 zzUndetermined_S0_L001_R1_001.fastq.gz29 | python /oak/stanford/groups/akundaje/marinovg/code/demultiplexFASTQDualIndex.py - SampleSheet-nonSHARE-seq.config 1 -prefix zz -suffix -L001-29
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py zzUndetermined_S0_L001_R1_001.fastq.gz3 zzUndetermined_S0_L001_R1_001.fastq.gz3 | python /oak/stanford/groups/akundaje/marinovg/code/demultiplexFASTQDualIndex.py - SampleSheet-nonSHARE-seq.config 1 -prefix zz -suffix -L001-3
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py zzUndetermined_S0_L001_R1_001.fastq.gz30 zzUndetermined_S0_L001_R1_001.fastq.gz30 | python /oak/stanford/groups/akundaje/marinovg/code/demultiplexFASTQDualIndex.py - SampleSheet-nonSHARE-seq.config 1 -prefix zz -suffix -L001-30
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py zzUndetermined_S0_L001_R1_001.fastq.gz31 zzUndetermined_S0_L001_R1_001.fastq.gz31 | python /oak/stanford/groups/akundaje/marinovg/code/demultiplexFASTQDualIndex.py - SampleSheet-nonSHARE-seq.config 1 -prefix zz -suffix -L001-31
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py zzUndetermined_S0_L001_R1_001.fastq.gz32 zzUndetermined_S0_L001_R1_001.fastq.gz32 | python /oak/stanford/groups/akundaje/marinovg/code/demultiplexFASTQDualIndex.py - SampleSheet-nonSHARE-seq.config 1 -prefix zz -suffix -L001-32
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py zzUndetermined_S0_L001_R1_001.fastq.gz33 zzUndetermined_S0_L001_R1_001.fastq.gz33 | python /oak/stanford/groups/akundaje/marinovg/code/demultiplexFASTQDualIndex.py - SampleSheet-nonSHARE-seq.config 1 -prefix zz -suffix -L001-33
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py zzUndetermined_S0_L001_R1_001.fastq.gz34 zzUndetermined_S0_L001_R1_001.fastq.gz34 | python /oak/stanford/groups/akundaje/marinovg/code/demultiplexFASTQDualIndex.py - SampleSheet-nonSHARE-seq.config 1 -prefix zz -suffix -L001-34
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py zzUndetermined_S0_L001_R1_001.fastq.gz35 zzUndetermined_S0_L001_R1_001.fastq.gz35 | python /oak/stanford/groups/akundaje/marinovg/code/demultiplexFASTQDualIndex.py - SampleSheet-nonSHARE-seq.config 1 -prefix zz -suffix -L001-35
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py zzUndetermined_S0_L001_R1_001.fastq.gz36 zzUndetermined_S0_L001_R1_001.fastq.gz36 | python /oak/stanford/groups/akundaje/marinovg/code/demultiplexFASTQDualIndex.py - SampleSheet-nonSHARE-seq.config 1 -prefix zz -suffix -L001-36
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py zzUndetermined_S0_L001_R1_001.fastq.gz37 zzUndetermined_S0_L001_R1_001.fastq.gz37 | python /oak/stanford/groups/akundaje/marinovg/code/demultiplexFASTQDualIndex.py - SampleSheet-nonSHARE-seq.config 1 -prefix zz -suffix -L001-37
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py zzUndetermined_S0_L001_R1_001.fastq.gz38 zzUndetermined_S0_L001_R1_001.fastq.gz38 | python /oak/stanford/groups/akundaje/marinovg/code/demultiplexFASTQDualIndex.py - SampleSheet-nonSHARE-seq.config 1 -prefix zz -suffix -L001-38
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py zzUndetermined_S0_L001_R1_001.fastq.gz39 zzUndetermined_S0_L001_R1_001.fastq.gz39 | python /oak/stanford/groups/akundaje/marinovg/code/demultiplexFASTQDualIndex.py - SampleSheet-nonSHARE-seq.config 1 -prefix zz -suffix -L001-39
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py zzUndetermined_S0_L001_R1_001.fastq.gz4 zzUndetermined_S0_L001_R1_001.fastq.gz4 | python /oak/stanford/groups/akundaje/marinovg/code/demultiplexFASTQDualIndex.py - SampleSheet-nonSHARE-seq.config 1 -prefix zz -suffix -L001-4
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py zzUndetermined_S0_L001_R1_001.fastq.gz40 zzUndetermined_S0_L001_R1_001.fastq.gz40 | python /oak/stanford/groups/akundaje/marinovg/code/demultiplexFASTQDualIndex.py - SampleSheet-nonSHARE-seq.config 1 -prefix zz -suffix -L001-40
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py zzUndetermined_S0_L001_R1_001.fastq.gz41 zzUndetermined_S0_L001_R1_001.fastq.gz41 | python /oak/stanford/groups/akundaje/marinovg/code/demultiplexFASTQDualIndex.py - SampleSheet-nonSHARE-seq.config 1 -prefix zz -suffix -L001-41
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py zzUndetermined_S0_L001_R1_001.fastq.gz42 zzUndetermined_S0_L001_R1_001.fastq.gz42 | python /oak/stanford/groups/akundaje/marinovg/code/demultiplexFASTQDualIndex.py - SampleSheet-nonSHARE-seq.config 1 -prefix zz -suffix -L001-42
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py zzUndetermined_S0_L001_R1_001.fastq.gz43 zzUndetermined_S0_L001_R1_001.fastq.gz43 | python /oak/stanford/groups/akundaje/marinovg/code/demultiplexFASTQDualIndex.py - SampleSheet-nonSHARE-seq.config 1 -prefix zz -suffix -L001-43
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py zzUndetermined_S0_L001_R1_001.fastq.gz44 zzUndetermined_S0_L001_R1_001.fastq.gz44 | python /oak/stanford/groups/akundaje/marinovg/code/demultiplexFASTQDualIndex.py - SampleSheet-nonSHARE-seq.config 1 -prefix zz -suffix -L001-44
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py zzUndetermined_S0_L001_R1_001.fastq.gz45 zzUndetermined_S0_L001_R1_001.fastq.gz45 | python /oak/stanford/groups/akundaje/marinovg/code/demultiplexFASTQDualIndex.py - SampleSheet-nonSHARE-seq.config 1 -prefix zz -suffix -L001-45
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py zzUndetermined_S0_L001_R1_001.fastq.gz46 zzUndetermined_S0_L001_R1_001.fastq.gz46 | python /oak/stanford/groups/akundaje/marinovg/code/demultiplexFASTQDualIndex.py - SampleSheet-nonSHARE-seq.config 1 -prefix zz -suffix -L001-46
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py zzUndetermined_S0_L001_R1_001.fastq.gz47 zzUndetermined_S0_L001_R1_001.fastq.gz47 | python /oak/stanford/groups/akundaje/marinovg/code/demultiplexFASTQDualIndex.py - SampleSheet-nonSHARE-seq.config 1 -prefix zz -suffix -L001-47
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py zzUndetermined_S0_L001_R1_001.fastq.gz48 zzUndetermined_S0_L001_R1_001.fastq.gz48 | python /oak/stanford/groups/akundaje/marinovg/code/demultiplexFASTQDualIndex.py - SampleSheet-nonSHARE-seq.config 1 -prefix zz -suffix -L001-48
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py zzUndetermined_S0_L001_R1_001.fastq.gz49 zzUndetermined_S0_L001_R1_001.fastq.gz49 | python /oak/stanford/groups/akundaje/marinovg/code/demultiplexFASTQDualIndex.py - SampleSheet-nonSHARE-seq.config 1 -prefix zz -suffix -L001-49
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py zzUndetermined_S0_L001_R1_001.fastq.gz5 zzUndetermined_S0_L001_R1_001.fastq.gz5 | python /oak/stanford/groups/akundaje/marinovg/code/demultiplexFASTQDualIndex.py - SampleSheet-nonSHARE-seq.config 1 -prefix zz -suffix -L001-5
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py zzUndetermined_S0_L001_R1_001.fastq.gz50 zzUndetermined_S0_L001_R1_001.fastq.gz50 | python /oak/stanford/groups/akundaje/marinovg/code/demultiplexFASTQDualIndex.py - SampleSheet-nonSHARE-seq.config 1 -prefix zz -suffix -L001-50
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py zzUndetermined_S0_L001_R1_001.fastq.gz51 zzUndetermined_S0_L001_R1_001.fastq.gz51 | python /oak/stanford/groups/akundaje/marinovg/code/demultiplexFASTQDualIndex.py - SampleSheet-nonSHARE-seq.config 1 -prefix zz -suffix -L001-51
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py zzUndetermined_S0_L001_R1_001.fastq.gz52 zzUndetermined_S0_L001_R1_001.fastq.gz52 | python /oak/stanford/groups/akundaje/marinovg/code/demultiplexFASTQDualIndex.py - SampleSheet-nonSHARE-seq.config 1 -prefix zz -suffix -L001-52
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py zzUndetermined_S0_L001_R1_001.fastq.gz53 zzUndetermined_S0_L001_R1_001.fastq.gz53 | python /oak/stanford/groups/akundaje/marinovg/code/demultiplexFASTQDualIndex.py - SampleSheet-nonSHARE-seq.config 1 -prefix zz -suffix -L001-53
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py zzUndetermined_S0_L001_R1_001.fastq.gz54 zzUndetermined_S0_L001_R1_001.fastq.gz54 | python /oak/stanford/groups/akundaje/marinovg/code/demultiplexFASTQDualIndex.py - SampleSheet-nonSHARE-seq.config 1 -prefix zz -suffix -L001-54
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py zzUndetermined_S0_L001_R1_001.fastq.gz55 zzUndetermined_S0_L001_R1_001.fastq.gz55 | python /oak/stanford/groups/akundaje/marinovg/code/demultiplexFASTQDualIndex.py - SampleSheet-nonSHARE-seq.config 1 -prefix zz -suffix -L001-55
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py zzUndetermined_S0_L001_R1_001.fastq.gz56 zzUndetermined_S0_L001_R1_001.fastq.gz56 | python /oak/stanford/groups/akundaje/marinovg/code/demultiplexFASTQDualIndex.py - SampleSheet-nonSHARE-seq.config 1 -prefix zz -suffix -L001-56
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py zzUndetermined_S0_L001_R1_001.fastq.gz57 zzUndetermined_S0_L001_R1_001.fastq.gz57 | python /oak/stanford/groups/akundaje/marinovg/code/demultiplexFASTQDualIndex.py - SampleSheet-nonSHARE-seq.config 1 -prefix zz -suffix -L001-57
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py zzUndetermined_S0_L001_R1_001.fastq.gz58 zzUndetermined_S0_L001_R1_001.fastq.gz58 | python /oak/stanford/groups/akundaje/marinovg/code/demultiplexFASTQDualIndex.py - SampleSheet-nonSHARE-seq.config 1 -prefix zz -suffix -L001-58
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py zzUndetermined_S0_L001_R1_001.fastq.gz59 zzUndetermined_S0_L001_R1_001.fastq.gz59 | python /oak/stanford/groups/akundaje/marinovg/code/demultiplexFASTQDualIndex.py - SampleSheet-nonSHARE-seq.config 1 -prefix zz -suffix -L001-59
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py zzUndetermined_S0_L001_R1_001.fastq.gz6 zzUndetermined_S0_L001_R1_001.fastq.gz6 | python /oak/stanford/groups/akundaje/marinovg/code/demultiplexFASTQDualIndex.py - SampleSheet-nonSHARE-seq.config 1 -prefix zz -suffix -L001-6
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py zzUndetermined_S0_L001_R1_001.fastq.gz60 zzUndetermined_S0_L001_R1_001.fastq.gz60 | python /oak/stanford/groups/akundaje/marinovg/code/demultiplexFASTQDualIndex.py - SampleSheet-nonSHARE-seq.config 1 -prefix zz -suffix -L001-60
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py zzUndetermined_S0_L001_R1_001.fastq.gz61 zzUndetermined_S0_L001_R1_001.fastq.gz61 | python /oak/stanford/groups/akundaje/marinovg/code/demultiplexFASTQDualIndex.py - SampleSheet-nonSHARE-seq.config 1 -prefix zz -suffix -L001-61
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py zzUndetermined_S0_L001_R1_001.fastq.gz62 zzUndetermined_S0_L001_R1_001.fastq.gz62 | python /oak/stanford/groups/akundaje/marinovg/code/demultiplexFASTQDualIndex.py - SampleSheet-nonSHARE-seq.config 1 -prefix zz -suffix -L001-62
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py zzUndetermined_S0_L001_R1_001.fastq.gz63 zzUndetermined_S0_L001_R1_001.fastq.gz63 | python /oak/stanford/groups/akundaje/marinovg/code/demultiplexFASTQDualIndex.py - SampleSheet-nonSHARE-seq.config 1 -prefix zz -suffix -L001-63
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py zzUndetermined_S0_L001_R1_001.fastq.gz64 zzUndetermined_S0_L001_R1_001.fastq.gz64 | python /oak/stanford/groups/akundaje/marinovg/code/demultiplexFASTQDualIndex.py - SampleSheet-nonSHARE-seq.config 1 -prefix zz -suffix -L001-64
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py zzUndetermined_S0_L001_R1_001.fastq.gz65 zzUndetermined_S0_L001_R1_001.fastq.gz65 | python /oak/stanford/groups/akundaje/marinovg/code/demultiplexFASTQDualIndex.py - SampleSheet-nonSHARE-seq.config 1 -prefix zz -suffix -L001-65
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py zzUndetermined_S0_L001_R1_001.fastq.gz66 zzUndetermined_S0_L001_R1_001.fastq.gz66 | python /oak/stanford/groups/akundaje/marinovg/code/demultiplexFASTQDualIndex.py - SampleSheet-nonSHARE-seq.config 1 -prefix zz -suffix -L001-66
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py zzUndetermined_S0_L001_R1_001.fastq.gz67 zzUndetermined_S0_L001_R1_001.fastq.gz67 | python /oak/stanford/groups/akundaje/marinovg/code/demultiplexFASTQDualIndex.py - SampleSheet-nonSHARE-seq.config 1 -prefix zz -suffix -L001-67
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py zzUndetermined_S0_L001_R1_001.fastq.gz68 zzUndetermined_S0_L001_R1_001.fastq.gz68 | python /oak/stanford/groups/akundaje/marinovg/code/demultiplexFASTQDualIndex.py - SampleSheet-nonSHARE-seq.config 1 -prefix zz -suffix -L001-68
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py zzUndetermined_S0_L001_R1_001.fastq.gz69 zzUndetermined_S0_L001_R1_001.fastq.gz69 | python /oak/stanford/groups/akundaje/marinovg/code/demultiplexFASTQDualIndex.py - SampleSheet-nonSHARE-seq.config 1 -prefix zz -suffix -L001-69
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py zzUndetermined_S0_L001_R1_001.fastq.gz7 zzUndetermined_S0_L001_R1_001.fastq.gz7 | python /oak/stanford/groups/akundaje/marinovg/code/demultiplexFASTQDualIndex.py - SampleSheet-nonSHARE-seq.config 1 -prefix zz -suffix -L001-7
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py zzUndetermined_S0_L001_R1_001.fastq.gz70 zzUndetermined_S0_L001_R1_001.fastq.gz70 | python /oak/stanford/groups/akundaje/marinovg/code/demultiplexFASTQDualIndex.py - SampleSheet-nonSHARE-seq.config 1 -prefix zz -suffix -L001-70
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py zzUndetermined_S0_L001_R1_001.fastq.gz71 zzUndetermined_S0_L001_R1_001.fastq.gz71 | python /oak/stanford/groups/akundaje/marinovg/code/demultiplexFASTQDualIndex.py - SampleSheet-nonSHARE-seq.config 1 -prefix zz -suffix -L001-71
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py zzUndetermined_S0_L001_R1_001.fastq.gz72 zzUndetermined_S0_L001_R1_001.fastq.gz72 | python /oak/stanford/groups/akundaje/marinovg/code/demultiplexFASTQDualIndex.py - SampleSheet-nonSHARE-seq.config 1 -prefix zz -suffix -L001-72
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py zzUndetermined_S0_L001_R1_001.fastq.gz73 zzUndetermined_S0_L001_R1_001.fastq.gz73 | python /oak/stanford/groups/akundaje/marinovg/code/demultiplexFASTQDualIndex.py - SampleSheet-nonSHARE-seq.config 1 -prefix zz -suffix -L001-73
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py zzUndetermined_S0_L001_R1_001.fastq.gz74 zzUndetermined_S0_L001_R1_001.fastq.gz74 | python /oak/stanford/groups/akundaje/marinovg/code/demultiplexFASTQDualIndex.py - SampleSheet-nonSHARE-seq.config 1 -prefix zz -suffix -L001-74
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py zzUndetermined_S0_L001_R1_001.fastq.gz75 zzUndetermined_S0_L001_R1_001.fastq.gz75 | python /oak/stanford/groups/akundaje/marinovg/code/demultiplexFASTQDualIndex.py - SampleSheet-nonSHARE-seq.config 1 -prefix zz -suffix -L001-75
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py zzUndetermined_S0_L001_R1_001.fastq.gz76 zzUndetermined_S0_L001_R1_001.fastq.gz76 | python /oak/stanford/groups/akundaje/marinovg/code/demultiplexFASTQDualIndex.py - SampleSheet-nonSHARE-seq.config 1 -prefix zz -suffix -L001-76
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py zzUndetermined_S0_L001_R1_001.fastq.gz77 zzUndetermined_S0_L001_R1_001.fastq.gz77 | python /oak/stanford/groups/akundaje/marinovg/code/demultiplexFASTQDualIndex.py - SampleSheet-nonSHARE-seq.config 1 -prefix zz -suffix -L001-77
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py zzUndetermined_S0_L001_R1_001.fastq.gz78 zzUndetermined_S0_L001_R1_001.fastq.gz78 | python /oak/stanford/groups/akundaje/marinovg/code/demultiplexFASTQDualIndex.py - SampleSheet-nonSHARE-seq.config 1 -prefix zz -suffix -L001-78
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py zzUndetermined_S0_L001_R1_001.fastq.gz79 zzUndetermined_S0_L001_R1_001.fastq.gz79 | python /oak/stanford/groups/akundaje/marinovg/code/demultiplexFASTQDualIndex.py - SampleSheet-nonSHARE-seq.config 1 -prefix zz -suffix -L001-79
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py zzUndetermined_S0_L001_R1_001.fastq.gz8 zzUndetermined_S0_L001_R1_001.fastq.gz8 | python /oak/stanford/groups/akundaje/marinovg/code/demultiplexFASTQDualIndex.py - SampleSheet-nonSHARE-seq.config 1 -prefix zz -suffix -L001-8
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py zzUndetermined_S0_L001_R1_001.fastq.gz80 zzUndetermined_S0_L001_R1_001.fastq.gz80 | python /oak/stanford/groups/akundaje/marinovg/code/demultiplexFASTQDualIndex.py - SampleSheet-nonSHARE-seq.config 1 -prefix zz -suffix -L001-80
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py zzUndetermined_S0_L001_R1_001.fastq.gz81 zzUndetermined_S0_L001_R1_001.fastq.gz81 | python /oak/stanford/groups/akundaje/marinovg/code/demultiplexFASTQDualIndex.py - SampleSheet-nonSHARE-seq.config 1 -prefix zz -suffix -L001-81
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py zzUndetermined_S0_L001_R1_001.fastq.gz82 zzUndetermined_S0_L001_R1_001.fastq.gz82 | python /oak/stanford/groups/akundaje/marinovg/code/demultiplexFASTQDualIndex.py - SampleSheet-nonSHARE-seq.config 1 -prefix zz -suffix -L001-82
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py zzUndetermined_S0_L001_R1_001.fastq.gz83 zzUndetermined_S0_L001_R1_001.fastq.gz83 | python /oak/stanford/groups/akundaje/marinovg/code/demultiplexFASTQDualIndex.py - SampleSheet-nonSHARE-seq.config 1 -prefix zz -suffix -L001-83
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py zzUndetermined_S0_L001_R1_001.fastq.gz84 zzUndetermined_S0_L001_R1_001.fastq.gz84 | python /oak/stanford/groups/akundaje/marinovg/code/demultiplexFASTQDualIndex.py - SampleSheet-nonSHARE-seq.config 1 -prefix zz -suffix -L001-84
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py zzUndetermined_S0_L001_R1_001.fastq.gz85 zzUndetermined_S0_L001_R1_001.fastq.gz85 | python /oak/stanford/groups/akundaje/marinovg/code/demultiplexFASTQDualIndex.py - SampleSheet-nonSHARE-seq.config 1 -prefix zz -suffix -L001-85
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py zzUndetermined_S0_L001_R1_001.fastq.gz86 zzUndetermined_S0_L001_R1_001.fastq.gz86 | python /oak/stanford/groups/akundaje/marinovg/code/demultiplexFASTQDualIndex.py - SampleSheet-nonSHARE-seq.config 1 -prefix zz -suffix -L001-86
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py zzUndetermined_S0_L001_R1_001.fastq.gz87 zzUndetermined_S0_L001_R1_001.fastq.gz87 | python /oak/stanford/groups/akundaje/marinovg/code/demultiplexFASTQDualIndex.py - SampleSheet-nonSHARE-seq.config 1 -prefix zz -suffix -L001-87
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py zzUndetermined_S0_L001_R1_001.fastq.gz88 zzUndetermined_S0_L001_R1_001.fastq.gz88 | python /oak/stanford/groups/akundaje/marinovg/code/demultiplexFASTQDualIndex.py - SampleSheet-nonSHARE-seq.config 1 -prefix zz -suffix -L001-88
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py zzUndetermined_S0_L001_R1_001.fastq.gz89 zzUndetermined_S0_L001_R1_001.fastq.gz89 | python /oak/stanford/groups/akundaje/marinovg/code/demultiplexFASTQDualIndex.py - SampleSheet-nonSHARE-seq.config 1 -prefix zz -suffix -L001-89
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py zzUndetermined_S0_L001_R1_001.fastq.gz9 zzUndetermined_S0_L001_R1_001.fastq.gz9 | python /oak/stanford/groups/akundaje/marinovg/code/demultiplexFASTQDualIndex.py - SampleSheet-nonSHARE-seq.config 1 -prefix zz -suffix -L001-9
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py zzUndetermined_S0_L001_R1_001.fastq.gz90 zzUndetermined_S0_L001_R1_001.fastq.gz90 | python /oak/stanford/groups/akundaje/marinovg/code/demultiplexFASTQDualIndex.py - SampleSheet-nonSHARE-seq.config 1 -prefix zz -suffix -L001-90
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py zzUndetermined_S0_L001_R1_001.fastq.gz91 zzUndetermined_S0_L001_R1_001.fastq.gz91 | python /oak/stanford/groups/akundaje/marinovg/code/demultiplexFASTQDualIndex.py - SampleSheet-nonSHARE-seq.config 1 -prefix zz -suffix -L001-91
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py zzUndetermined_S0_L001_R1_001.fastq.gz92 zzUndetermined_S0_L001_R1_001.fastq.gz92 | python /oak/stanford/groups/akundaje/marinovg/code/demultiplexFASTQDualIndex.py - SampleSheet-nonSHARE-seq.config 1 -prefix zz -suffix -L001-92
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py zzUndetermined_S0_L001_R1_001.fastq.gz93 zzUndetermined_S0_L001_R1_001.fastq.gz93 | python /oak/stanford/groups/akundaje/marinovg/code/demultiplexFASTQDualIndex.py - SampleSheet-nonSHARE-seq.config 1 -prefix zz -suffix -L001-93
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py zzUndetermined_S0_L001_R1_001.fastq.gz94 zzUndetermined_S0_L001_R1_001.fastq.gz94 | python /oak/stanford/groups/akundaje/marinovg/code/demultiplexFASTQDualIndex.py - SampleSheet-nonSHARE-seq.config 1 -prefix zz -suffix -L001-94
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py zzUndetermined_S0_L001_R1_001.fastq.gz95 zzUndetermined_S0_L001_R1_001.fastq.gz95 | python /oak/stanford/groups/akundaje/marinovg/code/demultiplexFASTQDualIndex.py - SampleSheet-nonSHARE-seq.config 1 -prefix zz -suffix -L001-95
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py zzUndetermined_S0_L001_R1_001.fastq.gz96 zzUndetermined_S0_L001_R1_001.fastq.gz96 | python /oak/stanford/groups/akundaje/marinovg/code/demultiplexFASTQDualIndex.py - SampleSheet-nonSHARE-seq.config 1 -prefix zz -suffix -L001-96
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py zzUndetermined_S0_L001_R1_001.fastq.gz97 zzUndetermined_S0_L001_R1_001.fastq.gz97 | python /oak/stanford/groups/akundaje/marinovg/code/demultiplexFASTQDualIndex.py - SampleSheet-nonSHARE-seq.config 1 -prefix zz -suffix -L001-97
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py zzUndetermined_S0_L001_R1_001.fastq.gz98 zzUndetermined_S0_L001_R1_001.fastq.gz98 | python /oak/stanford/groups/akundaje/marinovg/code/demultiplexFASTQDualIndex.py - SampleSheet-nonSHARE-seq.config 1 -prefix zz -suffix -L001-98
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py zzUndetermined_S0_L001_R1_001.fastq.gz99 zzUndetermined_S0_L001_R1_001.fastq.gz99 | python /oak/stanford/groups/akundaje/marinovg/code/demultiplexFASTQDualIndex.py - SampleSheet-nonSHARE-seq.config 1 -prefix zz -suffix -L001-99
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py zzUndetermined_S0_L002_R1_001.fastq.gz0 zzUndetermined_S0_L002_R1_001.fastq.gz0 | python /oak/stanford/groups/akundaje/marinovg/code/demultiplexFASTQDualIndex.py - SampleSheet-nonSHARE-seq.config 1 -prefix zz -suffix -L002-0
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py zzUndetermined_S0_L002_R1_001.fastq.gz1 zzUndetermined_S0_L002_R1_001.fastq.gz1 | python /oak/stanford/groups/akundaje/marinovg/code/demultiplexFASTQDualIndex.py - SampleSheet-nonSHARE-seq.config 1 -prefix zz -suffix -L002-1
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py zzUndetermined_S0_L002_R1_001.fastq.gz10 zzUndetermined_S0_L002_R1_001.fastq.gz10 | python /oak/stanford/groups/akundaje/marinovg/code/demultiplexFASTQDualIndex.py - SampleSheet-nonSHARE-seq.config 1 -prefix zz -suffix -L002-10
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py zzUndetermined_S0_L002_R1_001.fastq.gz100 zzUndetermined_S0_L002_R1_001.fastq.gz100 | python /oak/stanford/groups/akundaje/marinovg/code/demultiplexFASTQDualIndex.py - SampleSheet-nonSHARE-seq.config 1 -prefix zz -suffix -L002-100
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py zzUndetermined_S0_L002_R1_001.fastq.gz101 zzUndetermined_S0_L002_R1_001.fastq.gz101 | python /oak/stanford/groups/akundaje/marinovg/code/demultiplexFASTQDualIndex.py - SampleSheet-nonSHARE-seq.config 1 -prefix zz -suffix -L002-101
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py zzUndetermined_S0_L002_R1_001.fastq.gz102 zzUndetermined_S0_L002_R1_001.fastq.gz102 | python /oak/stanford/groups/akundaje/marinovg/code/demultiplexFASTQDualIndex.py - SampleSheet-nonSHARE-seq.config 1 -prefix zz -suffix -L002-102
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py zzUndetermined_S0_L002_R1_001.fastq.gz103 zzUndetermined_S0_L002_R1_001.fastq.gz103 | python /oak/stanford/groups/akundaje/marinovg/code/demultiplexFASTQDualIndex.py - SampleSheet-nonSHARE-seq.config 1 -prefix zz -suffix -L002-103
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py zzUndetermined_S0_L002_R1_001.fastq.gz104 zzUndetermined_S0_L002_R1_001.fastq.gz104 | python /oak/stanford/groups/akundaje/marinovg/code/demultiplexFASTQDualIndex.py - SampleSheet-nonSHARE-seq.config 1 -prefix zz -suffix -L002-104
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py zzUndetermined_S0_L002_R1_001.fastq.gz105 zzUndetermined_S0_L002_R1_001.fastq.gz105 | python /oak/stanford/groups/akundaje/marinovg/code/demultiplexFASTQDualIndex.py - SampleSheet-nonSHARE-seq.config 1 -prefix zz -suffix -L002-105
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py zzUndetermined_S0_L002_R1_001.fastq.gz106 zzUndetermined_S0_L002_R1_001.fastq.gz106 | python /oak/stanford/groups/akundaje/marinovg/code/demultiplexFASTQDualIndex.py - SampleSheet-nonSHARE-seq.config 1 -prefix zz -suffix -L002-106
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py zzUndetermined_S0_L002_R1_001.fastq.gz107 zzUndetermined_S0_L002_R1_001.fastq.gz107 | python /oak/stanford/groups/akundaje/marinovg/code/demultiplexFASTQDualIndex.py - SampleSheet-nonSHARE-seq.config 1 -prefix zz -suffix -L002-107
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py zzUndetermined_S0_L002_R1_001.fastq.gz108 zzUndetermined_S0_L002_R1_001.fastq.gz108 | python /oak/stanford/groups/akundaje/marinovg/code/demultiplexFASTQDualIndex.py - SampleSheet-nonSHARE-seq.config 1 -prefix zz -suffix -L002-108
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py zzUndetermined_S0_L002_R1_001.fastq.gz109 zzUndetermined_S0_L002_R1_001.fastq.gz109 | python /oak/stanford/groups/akundaje/marinovg/code/demultiplexFASTQDualIndex.py - SampleSheet-nonSHARE-seq.config 1 -prefix zz -suffix -L002-109
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py zzUndetermined_S0_L002_R1_001.fastq.gz11 zzUndetermined_S0_L002_R1_001.fastq.gz11 | python /oak/stanford/groups/akundaje/marinovg/code/demultiplexFASTQDualIndex.py - SampleSheet-nonSHARE-seq.config 1 -prefix zz -suffix -L002-11
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py zzUndetermined_S0_L002_R1_001.fastq.gz110 zzUndetermined_S0_L002_R1_001.fastq.gz110 | python /oak/stanford/groups/akundaje/marinovg/code/demultiplexFASTQDualIndex.py - SampleSheet-nonSHARE-seq.config 1 -prefix zz -suffix -L002-110
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py zzUndetermined_S0_L002_R1_001.fastq.gz111 zzUndetermined_S0_L002_R1_001.fastq.gz111 | python /oak/stanford/groups/akundaje/marinovg/code/demultiplexFASTQDualIndex.py - SampleSheet-nonSHARE-seq.config 1 -prefix zz -suffix -L002-111
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py zzUndetermined_S0_L002_R1_001.fastq.gz112 zzUndetermined_S0_L002_R1_001.fastq.gz112 | python /oak/stanford/groups/akundaje/marinovg/code/demultiplexFASTQDualIndex.py - SampleSheet-nonSHARE-seq.config 1 -prefix zz -suffix -L002-112
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py zzUndetermined_S0_L002_R1_001.fastq.gz113 zzUndetermined_S0_L002_R1_001.fastq.gz113 | python /oak/stanford/groups/akundaje/marinovg/code/demultiplexFASTQDualIndex.py - SampleSheet-nonSHARE-seq.config 1 -prefix zz -suffix -L002-113
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py zzUndetermined_S0_L002_R1_001.fastq.gz114 zzUndetermined_S0_L002_R1_001.fastq.gz114 | python /oak/stanford/groups/akundaje/marinovg/code/demultiplexFASTQDualIndex.py - SampleSheet-nonSHARE-seq.config 1 -prefix zz -suffix -L002-114
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py zzUndetermined_S0_L002_R1_001.fastq.gz115 zzUndetermined_S0_L002_R1_001.fastq.gz115 | python /oak/stanford/groups/akundaje/marinovg/code/demultiplexFASTQDualIndex.py - SampleSheet-nonSHARE-seq.config 1 -prefix zz -suffix -L002-115
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py zzUndetermined_S0_L002_R1_001.fastq.gz116 zzUndetermined_S0_L002_R1_001.fastq.gz116 | python /oak/stanford/groups/akundaje/marinovg/code/demultiplexFASTQDualIndex.py - SampleSheet-nonSHARE-seq.config 1 -prefix zz -suffix -L002-116
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py zzUndetermined_S0_L002_R1_001.fastq.gz117 zzUndetermined_S0_L002_R1_001.fastq.gz117 | python /oak/stanford/groups/akundaje/marinovg/code/demultiplexFASTQDualIndex.py - SampleSheet-nonSHARE-seq.config 1 -prefix zz -suffix -L002-117
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py zzUndetermined_S0_L002_R1_001.fastq.gz118 zzUndetermined_S0_L002_R1_001.fastq.gz118 | python /oak/stanford/groups/akundaje/marinovg/code/demultiplexFASTQDualIndex.py - SampleSheet-nonSHARE-seq.config 1 -prefix zz -suffix -L002-118
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py zzUndetermined_S0_L002_R1_001.fastq.gz119 zzUndetermined_S0_L002_R1_001.fastq.gz119 | python /oak/stanford/groups/akundaje/marinovg/code/demultiplexFASTQDualIndex.py - SampleSheet-nonSHARE-seq.config 1 -prefix zz -suffix -L002-119
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py zzUndetermined_S0_L002_R1_001.fastq.gz12 zzUndetermined_S0_L002_R1_001.fastq.gz12 | python /oak/stanford/groups/akundaje/marinovg/code/demultiplexFASTQDualIndex.py - SampleSheet-nonSHARE-seq.config 1 -prefix zz -suffix -L002-12
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py zzUndetermined_S0_L002_R1_001.fastq.gz120 zzUndetermined_S0_L002_R1_001.fastq.gz120 | python /oak/stanford/groups/akundaje/marinovg/code/demultiplexFASTQDualIndex.py - SampleSheet-nonSHARE-seq.config 1 -prefix zz -suffix -L002-120
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py zzUndetermined_S0_L002_R1_001.fastq.gz121 zzUndetermined_S0_L002_R1_001.fastq.gz121 | python /oak/stanford/groups/akundaje/marinovg/code/demultiplexFASTQDualIndex.py - SampleSheet-nonSHARE-seq.config 1 -prefix zz -suffix -L002-121
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py zzUndetermined_S0_L002_R1_001.fastq.gz122 zzUndetermined_S0_L002_R1_001.fastq.gz122 | python /oak/stanford/groups/akundaje/marinovg/code/demultiplexFASTQDualIndex.py - SampleSheet-nonSHARE-seq.config 1 -prefix zz -suffix -L002-122
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py zzUndetermined_S0_L002_R1_001.fastq.gz123 zzUndetermined_S0_L002_R1_001.fastq.gz123 | python /oak/stanford/groups/akundaje/marinovg/code/demultiplexFASTQDualIndex.py - SampleSheet-nonSHARE-seq.config 1 -prefix zz -suffix -L002-123
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py zzUndetermined_S0_L002_R1_001.fastq.gz124 zzUndetermined_S0_L002_R1_001.fastq.gz124 | python /oak/stanford/groups/akundaje/marinovg/code/demultiplexFASTQDualIndex.py - SampleSheet-nonSHARE-seq.config 1 -prefix zz -suffix -L002-124
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py zzUndetermined_S0_L002_R1_001.fastq.gz125 zzUndetermined_S0_L002_R1_001.fastq.gz125 | python /oak/stanford/groups/akundaje/marinovg/code/demultiplexFASTQDualIndex.py - SampleSheet-nonSHARE-seq.config 1 -prefix zz -suffix -L002-125
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py zzUndetermined_S0_L002_R1_001.fastq.gz126 zzUndetermined_S0_L002_R1_001.fastq.gz126 | python /oak/stanford/groups/akundaje/marinovg/code/demultiplexFASTQDualIndex.py - SampleSheet-nonSHARE-seq.config 1 -prefix zz -suffix -L002-126
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py zzUndetermined_S0_L002_R1_001.fastq.gz127 zzUndetermined_S0_L002_R1_001.fastq.gz127 | python /oak/stanford/groups/akundaje/marinovg/code/demultiplexFASTQDualIndex.py - SampleSheet-nonSHARE-seq.config 1 -prefix zz -suffix -L002-127
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py zzUndetermined_S0_L002_R1_001.fastq.gz128 zzUndetermined_S0_L002_R1_001.fastq.gz128 | python /oak/stanford/groups/akundaje/marinovg/code/demultiplexFASTQDualIndex.py - SampleSheet-nonSHARE-seq.config 1 -prefix zz -suffix -L002-128
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py zzUndetermined_S0_L002_R1_001.fastq.gz13 zzUndetermined_S0_L002_R1_001.fastq.gz13 | python /oak/stanford/groups/akundaje/marinovg/code/demultiplexFASTQDualIndex.py - SampleSheet-nonSHARE-seq.config 1 -prefix zz -suffix -L002-13
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py zzUndetermined_S0_L002_R1_001.fastq.gz14 zzUndetermined_S0_L002_R1_001.fastq.gz14 | python /oak/stanford/groups/akundaje/marinovg/code/demultiplexFASTQDualIndex.py - SampleSheet-nonSHARE-seq.config 1 -prefix zz -suffix -L002-14
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py zzUndetermined_S0_L002_R1_001.fastq.gz15 zzUndetermined_S0_L002_R1_001.fastq.gz15 | python /oak/stanford/groups/akundaje/marinovg/code/demultiplexFASTQDualIndex.py - SampleSheet-nonSHARE-seq.config 1 -prefix zz -suffix -L002-15
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py zzUndetermined_S0_L002_R1_001.fastq.gz16 zzUndetermined_S0_L002_R1_001.fastq.gz16 | python /oak/stanford/groups/akundaje/marinovg/code/demultiplexFASTQDualIndex.py - SampleSheet-nonSHARE-seq.config 1 -prefix zz -suffix -L002-16
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py zzUndetermined_S0_L002_R1_001.fastq.gz17 zzUndetermined_S0_L002_R1_001.fastq.gz17 | python /oak/stanford/groups/akundaje/marinovg/code/demultiplexFASTQDualIndex.py - SampleSheet-nonSHARE-seq.config 1 -prefix zz -suffix -L002-17
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py zzUndetermined_S0_L002_R1_001.fastq.gz18 zzUndetermined_S0_L002_R1_001.fastq.gz18 | python /oak/stanford/groups/akundaje/marinovg/code/demultiplexFASTQDualIndex.py - SampleSheet-nonSHARE-seq.config 1 -prefix zz -suffix -L002-18
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py zzUndetermined_S0_L002_R1_001.fastq.gz19 zzUndetermined_S0_L002_R1_001.fastq.gz19 | python /oak/stanford/groups/akundaje/marinovg/code/demultiplexFASTQDualIndex.py - SampleSheet-nonSHARE-seq.config 1 -prefix zz -suffix -L002-19
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py zzUndetermined_S0_L002_R1_001.fastq.gz2 zzUndetermined_S0_L002_R1_001.fastq.gz2 | python /oak/stanford/groups/akundaje/marinovg/code/demultiplexFASTQDualIndex.py - SampleSheet-nonSHARE-seq.config 1 -prefix zz -suffix -L002-2
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py zzUndetermined_S0_L002_R1_001.fastq.gz20 zzUndetermined_S0_L002_R1_001.fastq.gz20 | python /oak/stanford/groups/akundaje/marinovg/code/demultiplexFASTQDualIndex.py - SampleSheet-nonSHARE-seq.config 1 -prefix zz -suffix -L002-20
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py zzUndetermined_S0_L002_R1_001.fastq.gz21 zzUndetermined_S0_L002_R1_001.fastq.gz21 | python /oak/stanford/groups/akundaje/marinovg/code/demultiplexFASTQDualIndex.py - SampleSheet-nonSHARE-seq.config 1 -prefix zz -suffix -L002-21
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py zzUndetermined_S0_L002_R1_001.fastq.gz22 zzUndetermined_S0_L002_R1_001.fastq.gz22 | python /oak/stanford/groups/akundaje/marinovg/code/demultiplexFASTQDualIndex.py - SampleSheet-nonSHARE-seq.config 1 -prefix zz -suffix -L002-22
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py zzUndetermined_S0_L002_R1_001.fastq.gz23 zzUndetermined_S0_L002_R1_001.fastq.gz23 | python /oak/stanford/groups/akundaje/marinovg/code/demultiplexFASTQDualIndex.py - SampleSheet-nonSHARE-seq.config 1 -prefix zz -suffix -L002-23
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py zzUndetermined_S0_L002_R1_001.fastq.gz24 zzUndetermined_S0_L002_R1_001.fastq.gz24 | python /oak/stanford/groups/akundaje/marinovg/code/demultiplexFASTQDualIndex.py - SampleSheet-nonSHARE-seq.config 1 -prefix zz -suffix -L002-24
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py zzUndetermined_S0_L002_R1_001.fastq.gz25 zzUndetermined_S0_L002_R1_001.fastq.gz25 | python /oak/stanford/groups/akundaje/marinovg/code/demultiplexFASTQDualIndex.py - SampleSheet-nonSHARE-seq.config 1 -prefix zz -suffix -L002-25
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py zzUndetermined_S0_L002_R1_001.fastq.gz26 zzUndetermined_S0_L002_R1_001.fastq.gz26 | python /oak/stanford/groups/akundaje/marinovg/code/demultiplexFASTQDualIndex.py - SampleSheet-nonSHARE-seq.config 1 -prefix zz -suffix -L002-26
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py zzUndetermined_S0_L002_R1_001.fastq.gz27 zzUndetermined_S0_L002_R1_001.fastq.gz27 | python /oak/stanford/groups/akundaje/marinovg/code/demultiplexFASTQDualIndex.py - SampleSheet-nonSHARE-seq.config 1 -prefix zz -suffix -L002-27
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py zzUndetermined_S0_L002_R1_001.fastq.gz28 zzUndetermined_S0_L002_R1_001.fastq.gz28 | python /oak/stanford/groups/akundaje/marinovg/code/demultiplexFASTQDualIndex.py - SampleSheet-nonSHARE-seq.config 1 -prefix zz -suffix -L002-28
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py zzUndetermined_S0_L002_R1_001.fastq.gz29 zzUndetermined_S0_L002_R1_001.fastq.gz29 | python /oak/stanford/groups/akundaje/marinovg/code/demultiplexFASTQDualIndex.py - SampleSheet-nonSHARE-seq.config 1 -prefix zz -suffix -L002-29
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py zzUndetermined_S0_L002_R1_001.fastq.gz3 zzUndetermined_S0_L002_R1_001.fastq.gz3 | python /oak/stanford/groups/akundaje/marinovg/code/demultiplexFASTQDualIndex.py - SampleSheet-nonSHARE-seq.config 1 -prefix zz -suffix -L002-3
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py zzUndetermined_S0_L002_R1_001.fastq.gz30 zzUndetermined_S0_L002_R1_001.fastq.gz30 | python /oak/stanford/groups/akundaje/marinovg/code/demultiplexFASTQDualIndex.py - SampleSheet-nonSHARE-seq.config 1 -prefix zz -suffix -L002-30
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py zzUndetermined_S0_L002_R1_001.fastq.gz31 zzUndetermined_S0_L002_R1_001.fastq.gz31 | python /oak/stanford/groups/akundaje/marinovg/code/demultiplexFASTQDualIndex.py - SampleSheet-nonSHARE-seq.config 1 -prefix zz -suffix -L002-31
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py zzUndetermined_S0_L002_R1_001.fastq.gz32 zzUndetermined_S0_L002_R1_001.fastq.gz32 | python /oak/stanford/groups/akundaje/marinovg/code/demultiplexFASTQDualIndex.py - SampleSheet-nonSHARE-seq.config 1 -prefix zz -suffix -L002-32
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py zzUndetermined_S0_L002_R1_001.fastq.gz33 zzUndetermined_S0_L002_R1_001.fastq.gz33 | python /oak/stanford/groups/akundaje/marinovg/code/demultiplexFASTQDualIndex.py - SampleSheet-nonSHARE-seq.config 1 -prefix zz -suffix -L002-33
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py zzUndetermined_S0_L002_R1_001.fastq.gz34 zzUndetermined_S0_L002_R1_001.fastq.gz34 | python /oak/stanford/groups/akundaje/marinovg/code/demultiplexFASTQDualIndex.py - SampleSheet-nonSHARE-seq.config 1 -prefix zz -suffix -L002-34
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py zzUndetermined_S0_L002_R1_001.fastq.gz35 zzUndetermined_S0_L002_R1_001.fastq.gz35 | python /oak/stanford/groups/akundaje/marinovg/code/demultiplexFASTQDualIndex.py - SampleSheet-nonSHARE-seq.config 1 -prefix zz -suffix -L002-35
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py zzUndetermined_S0_L002_R1_001.fastq.gz36 zzUndetermined_S0_L002_R1_001.fastq.gz36 | python /oak/stanford/groups/akundaje/marinovg/code/demultiplexFASTQDualIndex.py - SampleSheet-nonSHARE-seq.config 1 -prefix zz -suffix -L002-36
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py zzUndetermined_S0_L002_R1_001.fastq.gz37 zzUndetermined_S0_L002_R1_001.fastq.gz37 | python /oak/stanford/groups/akundaje/marinovg/code/demultiplexFASTQDualIndex.py - SampleSheet-nonSHARE-seq.config 1 -prefix zz -suffix -L002-37
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py zzUndetermined_S0_L002_R1_001.fastq.gz38 zzUndetermined_S0_L002_R1_001.fastq.gz38 | python /oak/stanford/groups/akundaje/marinovg/code/demultiplexFASTQDualIndex.py - SampleSheet-nonSHARE-seq.config 1 -prefix zz -suffix -L002-38
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py zzUndetermined_S0_L002_R1_001.fastq.gz39 zzUndetermined_S0_L002_R1_001.fastq.gz39 | python /oak/stanford/groups/akundaje/marinovg/code/demultiplexFASTQDualIndex.py - SampleSheet-nonSHARE-seq.config 1 -prefix zz -suffix -L002-39
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py zzUndetermined_S0_L002_R1_001.fastq.gz4 zzUndetermined_S0_L002_R1_001.fastq.gz4 | python /oak/stanford/groups/akundaje/marinovg/code/demultiplexFASTQDualIndex.py - SampleSheet-nonSHARE-seq.config 1 -prefix zz -suffix -L002-4
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py zzUndetermined_S0_L002_R1_001.fastq.gz40 zzUndetermined_S0_L002_R1_001.fastq.gz40 | python /oak/stanford/groups/akundaje/marinovg/code/demultiplexFASTQDualIndex.py - SampleSheet-nonSHARE-seq.config 1 -prefix zz -suffix -L002-40
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py zzUndetermined_S0_L002_R1_001.fastq.gz41 zzUndetermined_S0_L002_R1_001.fastq.gz41 | python /oak/stanford/groups/akundaje/marinovg/code/demultiplexFASTQDualIndex.py - SampleSheet-nonSHARE-seq.config 1 -prefix zz -suffix -L002-41
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py zzUndetermined_S0_L002_R1_001.fastq.gz42 zzUndetermined_S0_L002_R1_001.fastq.gz42 | python /oak/stanford/groups/akundaje/marinovg/code/demultiplexFASTQDualIndex.py - SampleSheet-nonSHARE-seq.config 1 -prefix zz -suffix -L002-42
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py zzUndetermined_S0_L002_R1_001.fastq.gz43 zzUndetermined_S0_L002_R1_001.fastq.gz43 | python /oak/stanford/groups/akundaje/marinovg/code/demultiplexFASTQDualIndex.py - SampleSheet-nonSHARE-seq.config 1 -prefix zz -suffix -L002-43
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py zzUndetermined_S0_L002_R1_001.fastq.gz44 zzUndetermined_S0_L002_R1_001.fastq.gz44 | python /oak/stanford/groups/akundaje/marinovg/code/demultiplexFASTQDualIndex.py - SampleSheet-nonSHARE-seq.config 1 -prefix zz -suffix -L002-44
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py zzUndetermined_S0_L002_R1_001.fastq.gz45 zzUndetermined_S0_L002_R1_001.fastq.gz45 | python /oak/stanford/groups/akundaje/marinovg/code/demultiplexFASTQDualIndex.py - SampleSheet-nonSHARE-seq.config 1 -prefix zz -suffix -L002-45
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py zzUndetermined_S0_L002_R1_001.fastq.gz46 zzUndetermined_S0_L002_R1_001.fastq.gz46 | python /oak/stanford/groups/akundaje/marinovg/code/demultiplexFASTQDualIndex.py - SampleSheet-nonSHARE-seq.config 1 -prefix zz -suffix -L002-46
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py zzUndetermined_S0_L002_R1_001.fastq.gz47 zzUndetermined_S0_L002_R1_001.fastq.gz47 | python /oak/stanford/groups/akundaje/marinovg/code/demultiplexFASTQDualIndex.py - SampleSheet-nonSHARE-seq.config 1 -prefix zz -suffix -L002-47
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py zzUndetermined_S0_L002_R1_001.fastq.gz48 zzUndetermined_S0_L002_R1_001.fastq.gz48 | python /oak/stanford/groups/akundaje/marinovg/code/demultiplexFASTQDualIndex.py - SampleSheet-nonSHARE-seq.config 1 -prefix zz -suffix -L002-48
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py zzUndetermined_S0_L002_R1_001.fastq.gz49 zzUndetermined_S0_L002_R1_001.fastq.gz49 | python /oak/stanford/groups/akundaje/marinovg/code/demultiplexFASTQDualIndex.py - SampleSheet-nonSHARE-seq.config 1 -prefix zz -suffix -L002-49
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py zzUndetermined_S0_L002_R1_001.fastq.gz5 zzUndetermined_S0_L002_R1_001.fastq.gz5 | python /oak/stanford/groups/akundaje/marinovg/code/demultiplexFASTQDualIndex.py - SampleSheet-nonSHARE-seq.config 1 -prefix zz -suffix -L002-5
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py zzUndetermined_S0_L002_R1_001.fastq.gz50 zzUndetermined_S0_L002_R1_001.fastq.gz50 | python /oak/stanford/groups/akundaje/marinovg/code/demultiplexFASTQDualIndex.py - SampleSheet-nonSHARE-seq.config 1 -prefix zz -suffix -L002-50
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py zzUndetermined_S0_L002_R1_001.fastq.gz51 zzUndetermined_S0_L002_R1_001.fastq.gz51 | python /oak/stanford/groups/akundaje/marinovg/code/demultiplexFASTQDualIndex.py - SampleSheet-nonSHARE-seq.config 1 -prefix zz -suffix -L002-51
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py zzUndetermined_S0_L002_R1_001.fastq.gz52 zzUndetermined_S0_L002_R1_001.fastq.gz52 | python /oak/stanford/groups/akundaje/marinovg/code/demultiplexFASTQDualIndex.py - SampleSheet-nonSHARE-seq.config 1 -prefix zz -suffix -L002-52
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py zzUndetermined_S0_L002_R1_001.fastq.gz53 zzUndetermined_S0_L002_R1_001.fastq.gz53 | python /oak/stanford/groups/akundaje/marinovg/code/demultiplexFASTQDualIndex.py - SampleSheet-nonSHARE-seq.config 1 -prefix zz -suffix -L002-53
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py zzUndetermined_S0_L002_R1_001.fastq.gz54 zzUndetermined_S0_L002_R1_001.fastq.gz54 | python /oak/stanford/groups/akundaje/marinovg/code/demultiplexFASTQDualIndex.py - SampleSheet-nonSHARE-seq.config 1 -prefix zz -suffix -L002-54
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py zzUndetermined_S0_L002_R1_001.fastq.gz55 zzUndetermined_S0_L002_R1_001.fastq.gz55 | python /oak/stanford/groups/akundaje/marinovg/code/demultiplexFASTQDualIndex.py - SampleSheet-nonSHARE-seq.config 1 -prefix zz -suffix -L002-55
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py zzUndetermined_S0_L002_R1_001.fastq.gz56 zzUndetermined_S0_L002_R1_001.fastq.gz56 | python /oak/stanford/groups/akundaje/marinovg/code/demultiplexFASTQDualIndex.py - SampleSheet-nonSHARE-seq.config 1 -prefix zz -suffix -L002-56
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py zzUndetermined_S0_L002_R1_001.fastq.gz57 zzUndetermined_S0_L002_R1_001.fastq.gz57 | python /oak/stanford/groups/akundaje/marinovg/code/demultiplexFASTQDualIndex.py - SampleSheet-nonSHARE-seq.config 1 -prefix zz -suffix -L002-57
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py zzUndetermined_S0_L002_R1_001.fastq.gz58 zzUndetermined_S0_L002_R1_001.fastq.gz58 | python /oak/stanford/groups/akundaje/marinovg/code/demultiplexFASTQDualIndex.py - SampleSheet-nonSHARE-seq.config 1 -prefix zz -suffix -L002-58
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py zzUndetermined_S0_L002_R1_001.fastq.gz59 zzUndetermined_S0_L002_R1_001.fastq.gz59 | python /oak/stanford/groups/akundaje/marinovg/code/demultiplexFASTQDualIndex.py - SampleSheet-nonSHARE-seq.config 1 -prefix zz -suffix -L002-59
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py zzUndetermined_S0_L002_R1_001.fastq.gz6 zzUndetermined_S0_L002_R1_001.fastq.gz6 | python /oak/stanford/groups/akundaje/marinovg/code/demultiplexFASTQDualIndex.py - SampleSheet-nonSHARE-seq.config 1 -prefix zz -suffix -L002-6
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py zzUndetermined_S0_L002_R1_001.fastq.gz60 zzUndetermined_S0_L002_R1_001.fastq.gz60 | python /oak/stanford/groups/akundaje/marinovg/code/demultiplexFASTQDualIndex.py - SampleSheet-nonSHARE-seq.config 1 -prefix zz -suffix -L002-60
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py zzUndetermined_S0_L002_R1_001.fastq.gz61 zzUndetermined_S0_L002_R1_001.fastq.gz61 | python /oak/stanford/groups/akundaje/marinovg/code/demultiplexFASTQDualIndex.py - SampleSheet-nonSHARE-seq.config 1 -prefix zz -suffix -L002-61
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py zzUndetermined_S0_L002_R1_001.fastq.gz62 zzUndetermined_S0_L002_R1_001.fastq.gz62 | python /oak/stanford/groups/akundaje/marinovg/code/demultiplexFASTQDualIndex.py - SampleSheet-nonSHARE-seq.config 1 -prefix zz -suffix -L002-62
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py zzUndetermined_S0_L002_R1_001.fastq.gz63 zzUndetermined_S0_L002_R1_001.fastq.gz63 | python /oak/stanford/groups/akundaje/marinovg/code/demultiplexFASTQDualIndex.py - SampleSheet-nonSHARE-seq.config 1 -prefix zz -suffix -L002-63
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py zzUndetermined_S0_L002_R1_001.fastq.gz64 zzUndetermined_S0_L002_R1_001.fastq.gz64 | python /oak/stanford/groups/akundaje/marinovg/code/demultiplexFASTQDualIndex.py - SampleSheet-nonSHARE-seq.config 1 -prefix zz -suffix -L002-64
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py zzUndetermined_S0_L002_R1_001.fastq.gz65 zzUndetermined_S0_L002_R1_001.fastq.gz65 | python /oak/stanford/groups/akundaje/marinovg/code/demultiplexFASTQDualIndex.py - SampleSheet-nonSHARE-seq.config 1 -prefix zz -suffix -L002-65
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py zzUndetermined_S0_L002_R1_001.fastq.gz66 zzUndetermined_S0_L002_R1_001.fastq.gz66 | python /oak/stanford/groups/akundaje/marinovg/code/demultiplexFASTQDualIndex.py - SampleSheet-nonSHARE-seq.config 1 -prefix zz -suffix -L002-66
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py zzUndetermined_S0_L002_R1_001.fastq.gz67 zzUndetermined_S0_L002_R1_001.fastq.gz67 | python /oak/stanford/groups/akundaje/marinovg/code/demultiplexFASTQDualIndex.py - SampleSheet-nonSHARE-seq.config 1 -prefix zz -suffix -L002-67
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py zzUndetermined_S0_L002_R1_001.fastq.gz68 zzUndetermined_S0_L002_R1_001.fastq.gz68 | python /oak/stanford/groups/akundaje/marinovg/code/demultiplexFASTQDualIndex.py - SampleSheet-nonSHARE-seq.config 1 -prefix zz -suffix -L002-68
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py zzUndetermined_S0_L002_R1_001.fastq.gz69 zzUndetermined_S0_L002_R1_001.fastq.gz69 | python /oak/stanford/groups/akundaje/marinovg/code/demultiplexFASTQDualIndex.py - SampleSheet-nonSHARE-seq.config 1 -prefix zz -suffix -L002-69
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py zzUndetermined_S0_L002_R1_001.fastq.gz7 zzUndetermined_S0_L002_R1_001.fastq.gz7 | python /oak/stanford/groups/akundaje/marinovg/code/demultiplexFASTQDualIndex.py - SampleSheet-nonSHARE-seq.config 1 -prefix zz -suffix -L002-7
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py zzUndetermined_S0_L002_R1_001.fastq.gz70 zzUndetermined_S0_L002_R1_001.fastq.gz70 | python /oak/stanford/groups/akundaje/marinovg/code/demultiplexFASTQDualIndex.py - SampleSheet-nonSHARE-seq.config 1 -prefix zz -suffix -L002-70
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py zzUndetermined_S0_L002_R1_001.fastq.gz71 zzUndetermined_S0_L002_R1_001.fastq.gz71 | python /oak/stanford/groups/akundaje/marinovg/code/demultiplexFASTQDualIndex.py - SampleSheet-nonSHARE-seq.config 1 -prefix zz -suffix -L002-71
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py zzUndetermined_S0_L002_R1_001.fastq.gz72 zzUndetermined_S0_L002_R1_001.fastq.gz72 | python /oak/stanford/groups/akundaje/marinovg/code/demultiplexFASTQDualIndex.py - SampleSheet-nonSHARE-seq.config 1 -prefix zz -suffix -L002-72
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py zzUndetermined_S0_L002_R1_001.fastq.gz73 zzUndetermined_S0_L002_R1_001.fastq.gz73 | python /oak/stanford/groups/akundaje/marinovg/code/demultiplexFASTQDualIndex.py - SampleSheet-nonSHARE-seq.config 1 -prefix zz -suffix -L002-73
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py zzUndetermined_S0_L002_R1_001.fastq.gz74 zzUndetermined_S0_L002_R1_001.fastq.gz74 | python /oak/stanford/groups/akundaje/marinovg/code/demultiplexFASTQDualIndex.py - SampleSheet-nonSHARE-seq.config 1 -prefix zz -suffix -L002-74
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py zzUndetermined_S0_L002_R1_001.fastq.gz75 zzUndetermined_S0_L002_R1_001.fastq.gz75 | python /oak/stanford/groups/akundaje/marinovg/code/demultiplexFASTQDualIndex.py - SampleSheet-nonSHARE-seq.config 1 -prefix zz -suffix -L002-75
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py zzUndetermined_S0_L002_R1_001.fastq.gz76 zzUndetermined_S0_L002_R1_001.fastq.gz76 | python /oak/stanford/groups/akundaje/marinovg/code/demultiplexFASTQDualIndex.py - SampleSheet-nonSHARE-seq.config 1 -prefix zz -suffix -L002-76
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py zzUndetermined_S0_L002_R1_001.fastq.gz77 zzUndetermined_S0_L002_R1_001.fastq.gz77 | python /oak/stanford/groups/akundaje/marinovg/code/demultiplexFASTQDualIndex.py - SampleSheet-nonSHARE-seq.config 1 -prefix zz -suffix -L002-77
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py zzUndetermined_S0_L002_R1_001.fastq.gz78 zzUndetermined_S0_L002_R1_001.fastq.gz78 | python /oak/stanford/groups/akundaje/marinovg/code/demultiplexFASTQDualIndex.py - SampleSheet-nonSHARE-seq.config 1 -prefix zz -suffix -L002-78
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py zzUndetermined_S0_L002_R1_001.fastq.gz79 zzUndetermined_S0_L002_R1_001.fastq.gz79 | python /oak/stanford/groups/akundaje/marinovg/code/demultiplexFASTQDualIndex.py - SampleSheet-nonSHARE-seq.config 1 -prefix zz -suffix -L002-79
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py zzUndetermined_S0_L002_R1_001.fastq.gz8 zzUndetermined_S0_L002_R1_001.fastq.gz8 | python /oak/stanford/groups/akundaje/marinovg/code/demultiplexFASTQDualIndex.py - SampleSheet-nonSHARE-seq.config 1 -prefix zz -suffix -L002-8
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py zzUndetermined_S0_L002_R1_001.fastq.gz80 zzUndetermined_S0_L002_R1_001.fastq.gz80 | python /oak/stanford/groups/akundaje/marinovg/code/demultiplexFASTQDualIndex.py - SampleSheet-nonSHARE-seq.config 1 -prefix zz -suffix -L002-80
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py zzUndetermined_S0_L002_R1_001.fastq.gz81 zzUndetermined_S0_L002_R1_001.fastq.gz81 | python /oak/stanford/groups/akundaje/marinovg/code/demultiplexFASTQDualIndex.py - SampleSheet-nonSHARE-seq.config 1 -prefix zz -suffix -L002-81
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py zzUndetermined_S0_L002_R1_001.fastq.gz82 zzUndetermined_S0_L002_R1_001.fastq.gz82 | python /oak/stanford/groups/akundaje/marinovg/code/demultiplexFASTQDualIndex.py - SampleSheet-nonSHARE-seq.config 1 -prefix zz -suffix -L002-82
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py zzUndetermined_S0_L002_R1_001.fastq.gz83 zzUndetermined_S0_L002_R1_001.fastq.gz83 | python /oak/stanford/groups/akundaje/marinovg/code/demultiplexFASTQDualIndex.py - SampleSheet-nonSHARE-seq.config 1 -prefix zz -suffix -L002-83
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py zzUndetermined_S0_L002_R1_001.fastq.gz84 zzUndetermined_S0_L002_R1_001.fastq.gz84 | python /oak/stanford/groups/akundaje/marinovg/code/demultiplexFASTQDualIndex.py - SampleSheet-nonSHARE-seq.config 1 -prefix zz -suffix -L002-84
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py zzUndetermined_S0_L002_R1_001.fastq.gz85 zzUndetermined_S0_L002_R1_001.fastq.gz85 | python /oak/stanford/groups/akundaje/marinovg/code/demultiplexFASTQDualIndex.py - SampleSheet-nonSHARE-seq.config 1 -prefix zz -suffix -L002-85
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py zzUndetermined_S0_L002_R1_001.fastq.gz86 zzUndetermined_S0_L002_R1_001.fastq.gz86 | python /oak/stanford/groups/akundaje/marinovg/code/demultiplexFASTQDualIndex.py - SampleSheet-nonSHARE-seq.config 1 -prefix zz -suffix -L002-86
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py zzUndetermined_S0_L002_R1_001.fastq.gz87 zzUndetermined_S0_L002_R1_001.fastq.gz87 | python /oak/stanford/groups/akundaje/marinovg/code/demultiplexFASTQDualIndex.py - SampleSheet-nonSHARE-seq.config 1 -prefix zz -suffix -L002-87
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py zzUndetermined_S0_L002_R1_001.fastq.gz88 zzUndetermined_S0_L002_R1_001.fastq.gz88 | python /oak/stanford/groups/akundaje/marinovg/code/demultiplexFASTQDualIndex.py - SampleSheet-nonSHARE-seq.config 1 -prefix zz -suffix -L002-88
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py zzUndetermined_S0_L002_R1_001.fastq.gz89 zzUndetermined_S0_L002_R1_001.fastq.gz89 | python /oak/stanford/groups/akundaje/marinovg/code/demultiplexFASTQDualIndex.py - SampleSheet-nonSHARE-seq.config 1 -prefix zz -suffix -L002-89
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py zzUndetermined_S0_L002_R1_001.fastq.gz9 zzUndetermined_S0_L002_R1_001.fastq.gz9 | python /oak/stanford/groups/akundaje/marinovg/code/demultiplexFASTQDualIndex.py - SampleSheet-nonSHARE-seq.config 1 -prefix zz -suffix -L002-9
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py zzUndetermined_S0_L002_R1_001.fastq.gz90 zzUndetermined_S0_L002_R1_001.fastq.gz90 | python /oak/stanford/groups/akundaje/marinovg/code/demultiplexFASTQDualIndex.py - SampleSheet-nonSHARE-seq.config 1 -prefix zz -suffix -L002-90
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py zzUndetermined_S0_L002_R1_001.fastq.gz91 zzUndetermined_S0_L002_R1_001.fastq.gz91 | python /oak/stanford/groups/akundaje/marinovg/code/demultiplexFASTQDualIndex.py - SampleSheet-nonSHARE-seq.config 1 -prefix zz -suffix -L002-91
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py zzUndetermined_S0_L002_R1_001.fastq.gz92 zzUndetermined_S0_L002_R1_001.fastq.gz92 | python /oak/stanford/groups/akundaje/marinovg/code/demultiplexFASTQDualIndex.py - SampleSheet-nonSHARE-seq.config 1 -prefix zz -suffix -L002-92
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py zzUndetermined_S0_L002_R1_001.fastq.gz93 zzUndetermined_S0_L002_R1_001.fastq.gz93 | python /oak/stanford/groups/akundaje/marinovg/code/demultiplexFASTQDualIndex.py - SampleSheet-nonSHARE-seq.config 1 -prefix zz -suffix -L002-93
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py zzUndetermined_S0_L002_R1_001.fastq.gz94 zzUndetermined_S0_L002_R1_001.fastq.gz94 | python /oak/stanford/groups/akundaje/marinovg/code/demultiplexFASTQDualIndex.py - SampleSheet-nonSHARE-seq.config 1 -prefix zz -suffix -L002-94
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py zzUndetermined_S0_L002_R1_001.fastq.gz95 zzUndetermined_S0_L002_R1_001.fastq.gz95 | python /oak/stanford/groups/akundaje/marinovg/code/demultiplexFASTQDualIndex.py - SampleSheet-nonSHARE-seq.config 1 -prefix zz -suffix -L002-95
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py zzUndetermined_S0_L002_R1_001.fastq.gz96 zzUndetermined_S0_L002_R1_001.fastq.gz96 | python /oak/stanford/groups/akundaje/marinovg/code/demultiplexFASTQDualIndex.py - SampleSheet-nonSHARE-seq.config 1 -prefix zz -suffix -L002-96
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py zzUndetermined_S0_L002_R1_001.fastq.gz97 zzUndetermined_S0_L002_R1_001.fastq.gz97 | python /oak/stanford/groups/akundaje/marinovg/code/demultiplexFASTQDualIndex.py - SampleSheet-nonSHARE-seq.config 1 -prefix zz -suffix -L002-97
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py zzUndetermined_S0_L002_R1_001.fastq.gz98 zzUndetermined_S0_L002_R1_001.fastq.gz98 | python /oak/stanford/groups/akundaje/marinovg/code/demultiplexFASTQDualIndex.py - SampleSheet-nonSHARE-seq.config 1 -prefix zz -suffix -L002-98
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py zzUndetermined_S0_L002_R1_001.fastq.gz99 zzUndetermined_S0_L002_R1_001.fastq.gz99 | python /oak/stanford/groups/akundaje/marinovg/code/demultiplexFASTQDualIndex.py - SampleSheet-nonSHARE-seq.config 1 -prefix zz -suffix -L002-99
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py zzUndetermined_S0_L003_R1_001.fastq.gz0 zzUndetermined_S0_L003_R1_001.fastq.gz0 | python /oak/stanford/groups/akundaje/marinovg/code/demultiplexFASTQDualIndex.py - SampleSheet-nonSHARE-seq.config 1 -prefix zz -suffix -L003-0
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py zzUndetermined_S0_L003_R1_001.fastq.gz1 zzUndetermined_S0_L003_R1_001.fastq.gz1 | python /oak/stanford/groups/akundaje/marinovg/code/demultiplexFASTQDualIndex.py - SampleSheet-nonSHARE-seq.config 1 -prefix zz -suffix -L003-1
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py zzUndetermined_S0_L003_R1_001.fastq.gz10 zzUndetermined_S0_L003_R1_001.fastq.gz10 | python /oak/stanford/groups/akundaje/marinovg/code/demultiplexFASTQDualIndex.py - SampleSheet-nonSHARE-seq.config 1 -prefix zz -suffix -L003-10
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py zzUndetermined_S0_L003_R1_001.fastq.gz100 zzUndetermined_S0_L003_R1_001.fastq.gz100 | python /oak/stanford/groups/akundaje/marinovg/code/demultiplexFASTQDualIndex.py - SampleSheet-nonSHARE-seq.config 1 -prefix zz -suffix -L003-100
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py zzUndetermined_S0_L003_R1_001.fastq.gz101 zzUndetermined_S0_L003_R1_001.fastq.gz101 | python /oak/stanford/groups/akundaje/marinovg/code/demultiplexFASTQDualIndex.py - SampleSheet-nonSHARE-seq.config 1 -prefix zz -suffix -L003-101
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py zzUndetermined_S0_L003_R1_001.fastq.gz102 zzUndetermined_S0_L003_R1_001.fastq.gz102 | python /oak/stanford/groups/akundaje/marinovg/code/demultiplexFASTQDualIndex.py - SampleSheet-nonSHARE-seq.config 1 -prefix zz -suffix -L003-102
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py zzUndetermined_S0_L003_R1_001.fastq.gz103 zzUndetermined_S0_L003_R1_001.fastq.gz103 | python /oak/stanford/groups/akundaje/marinovg/code/demultiplexFASTQDualIndex.py - SampleSheet-nonSHARE-seq.config 1 -prefix zz -suffix -L003-103
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py zzUndetermined_S0_L003_R1_001.fastq.gz104 zzUndetermined_S0_L003_R1_001.fastq.gz104 | python /oak/stanford/groups/akundaje/marinovg/code/demultiplexFASTQDualIndex.py - SampleSheet-nonSHARE-seq.config 1 -prefix zz -suffix -L003-104
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py zzUndetermined_S0_L003_R1_001.fastq.gz105 zzUndetermined_S0_L003_R1_001.fastq.gz105 | python /oak/stanford/groups/akundaje/marinovg/code/demultiplexFASTQDualIndex.py - SampleSheet-nonSHARE-seq.config 1 -prefix zz -suffix -L003-105
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py zzUndetermined_S0_L003_R1_001.fastq.gz106 zzUndetermined_S0_L003_R1_001.fastq.gz106 | python /oak/stanford/groups/akundaje/marinovg/code/demultiplexFASTQDualIndex.py - SampleSheet-nonSHARE-seq.config 1 -prefix zz -suffix -L003-106
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py zzUndetermined_S0_L003_R1_001.fastq.gz107 zzUndetermined_S0_L003_R1_001.fastq.gz107 | python /oak/stanford/groups/akundaje/marinovg/code/demultiplexFASTQDualIndex.py - SampleSheet-nonSHARE-seq.config 1 -prefix zz -suffix -L003-107
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py zzUndetermined_S0_L003_R1_001.fastq.gz108 zzUndetermined_S0_L003_R1_001.fastq.gz108 | python /oak/stanford/groups/akundaje/marinovg/code/demultiplexFASTQDualIndex.py - SampleSheet-nonSHARE-seq.config 1 -prefix zz -suffix -L003-108
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py zzUndetermined_S0_L003_R1_001.fastq.gz109 zzUndetermined_S0_L003_R1_001.fastq.gz109 | python /oak/stanford/groups/akundaje/marinovg/code/demultiplexFASTQDualIndex.py - SampleSheet-nonSHARE-seq.config 1 -prefix zz -suffix -L003-109
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py zzUndetermined_S0_L003_R1_001.fastq.gz11 zzUndetermined_S0_L003_R1_001.fastq.gz11 | python /oak/stanford/groups/akundaje/marinovg/code/demultiplexFASTQDualIndex.py - SampleSheet-nonSHARE-seq.config 1 -prefix zz -suffix -L003-11
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py zzUndetermined_S0_L003_R1_001.fastq.gz110 zzUndetermined_S0_L003_R1_001.fastq.gz110 | python /oak/stanford/groups/akundaje/marinovg/code/demultiplexFASTQDualIndex.py - SampleSheet-nonSHARE-seq.config 1 -prefix zz -suffix -L003-110
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py zzUndetermined_S0_L003_R1_001.fastq.gz111 zzUndetermined_S0_L003_R1_001.fastq.gz111 | python /oak/stanford/groups/akundaje/marinovg/code/demultiplexFASTQDualIndex.py - SampleSheet-nonSHARE-seq.config 1 -prefix zz -suffix -L003-111
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py zzUndetermined_S0_L003_R1_001.fastq.gz112 zzUndetermined_S0_L003_R1_001.fastq.gz112 | python /oak/stanford/groups/akundaje/marinovg/code/demultiplexFASTQDualIndex.py - SampleSheet-nonSHARE-seq.config 1 -prefix zz -suffix -L003-112
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py zzUndetermined_S0_L003_R1_001.fastq.gz113 zzUndetermined_S0_L003_R1_001.fastq.gz113 | python /oak/stanford/groups/akundaje/marinovg/code/demultiplexFASTQDualIndex.py - SampleSheet-nonSHARE-seq.config 1 -prefix zz -suffix -L003-113
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py zzUndetermined_S0_L003_R1_001.fastq.gz114 zzUndetermined_S0_L003_R1_001.fastq.gz114 | python /oak/stanford/groups/akundaje/marinovg/code/demultiplexFASTQDualIndex.py - SampleSheet-nonSHARE-seq.config 1 -prefix zz -suffix -L003-114
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py zzUndetermined_S0_L003_R1_001.fastq.gz115 zzUndetermined_S0_L003_R1_001.fastq.gz115 | python /oak/stanford/groups/akundaje/marinovg/code/demultiplexFASTQDualIndex.py - SampleSheet-nonSHARE-seq.config 1 -prefix zz -suffix -L003-115
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py zzUndetermined_S0_L003_R1_001.fastq.gz116 zzUndetermined_S0_L003_R1_001.fastq.gz116 | python /oak/stanford/groups/akundaje/marinovg/code/demultiplexFASTQDualIndex.py - SampleSheet-nonSHARE-seq.config 1 -prefix zz -suffix -L003-116
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py zzUndetermined_S0_L003_R1_001.fastq.gz117 zzUndetermined_S0_L003_R1_001.fastq.gz117 | python /oak/stanford/groups/akundaje/marinovg/code/demultiplexFASTQDualIndex.py - SampleSheet-nonSHARE-seq.config 1 -prefix zz -suffix -L003-117
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py zzUndetermined_S0_L003_R1_001.fastq.gz118 zzUndetermined_S0_L003_R1_001.fastq.gz118 | python /oak/stanford/groups/akundaje/marinovg/code/demultiplexFASTQDualIndex.py - SampleSheet-nonSHARE-seq.config 1 -prefix zz -suffix -L003-118
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py zzUndetermined_S0_L003_R1_001.fastq.gz119 zzUndetermined_S0_L003_R1_001.fastq.gz119 | python /oak/stanford/groups/akundaje/marinovg/code/demultiplexFASTQDualIndex.py - SampleSheet-nonSHARE-seq.config 1 -prefix zz -suffix -L003-119
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py zzUndetermined_S0_L003_R1_001.fastq.gz12 zzUndetermined_S0_L003_R1_001.fastq.gz12 | python /oak/stanford/groups/akundaje/marinovg/code/demultiplexFASTQDualIndex.py - SampleSheet-nonSHARE-seq.config 1 -prefix zz -suffix -L003-12
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py zzUndetermined_S0_L003_R1_001.fastq.gz120 zzUndetermined_S0_L003_R1_001.fastq.gz120 | python /oak/stanford/groups/akundaje/marinovg/code/demultiplexFASTQDualIndex.py - SampleSheet-nonSHARE-seq.config 1 -prefix zz -suffix -L003-120
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py zzUndetermined_S0_L003_R1_001.fastq.gz121 zzUndetermined_S0_L003_R1_001.fastq.gz121 | python /oak/stanford/groups/akundaje/marinovg/code/demultiplexFASTQDualIndex.py - SampleSheet-nonSHARE-seq.config 1 -prefix zz -suffix -L003-121
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py zzUndetermined_S0_L003_R1_001.fastq.gz122 zzUndetermined_S0_L003_R1_001.fastq.gz122 | python /oak/stanford/groups/akundaje/marinovg/code/demultiplexFASTQDualIndex.py - SampleSheet-nonSHARE-seq.config 1 -prefix zz -suffix -L003-122
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py zzUndetermined_S0_L003_R1_001.fastq.gz123 zzUndetermined_S0_L003_R1_001.fastq.gz123 | python /oak/stanford/groups/akundaje/marinovg/code/demultiplexFASTQDualIndex.py - SampleSheet-nonSHARE-seq.config 1 -prefix zz -suffix -L003-123
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py zzUndetermined_S0_L003_R1_001.fastq.gz124 zzUndetermined_S0_L003_R1_001.fastq.gz124 | python /oak/stanford/groups/akundaje/marinovg/code/demultiplexFASTQDualIndex.py - SampleSheet-nonSHARE-seq.config 1 -prefix zz -suffix -L003-124
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py zzUndetermined_S0_L003_R1_001.fastq.gz125 zzUndetermined_S0_L003_R1_001.fastq.gz125 | python /oak/stanford/groups/akundaje/marinovg/code/demultiplexFASTQDualIndex.py - SampleSheet-nonSHARE-seq.config 1 -prefix zz -suffix -L003-125
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py zzUndetermined_S0_L003_R1_001.fastq.gz126 zzUndetermined_S0_L003_R1_001.fastq.gz126 | python /oak/stanford/groups/akundaje/marinovg/code/demultiplexFASTQDualIndex.py - SampleSheet-nonSHARE-seq.config 1 -prefix zz -suffix -L003-126
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py zzUndetermined_S0_L003_R1_001.fastq.gz127 zzUndetermined_S0_L003_R1_001.fastq.gz127 | python /oak/stanford/groups/akundaje/marinovg/code/demultiplexFASTQDualIndex.py - SampleSheet-nonSHARE-seq.config 1 -prefix zz -suffix -L003-127
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py zzUndetermined_S0_L003_R1_001.fastq.gz128 zzUndetermined_S0_L003_R1_001.fastq.gz128 | python /oak/stanford/groups/akundaje/marinovg/code/demultiplexFASTQDualIndex.py - SampleSheet-nonSHARE-seq.config 1 -prefix zz -suffix -L003-128
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py zzUndetermined_S0_L003_R1_001.fastq.gz129 zzUndetermined_S0_L003_R1_001.fastq.gz129 | python /oak/stanford/groups/akundaje/marinovg/code/demultiplexFASTQDualIndex.py - SampleSheet-nonSHARE-seq.config 1 -prefix zz -suffix -L003-129
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py zzUndetermined_S0_L003_R1_001.fastq.gz13 zzUndetermined_S0_L003_R1_001.fastq.gz13 | python /oak/stanford/groups/akundaje/marinovg/code/demultiplexFASTQDualIndex.py - SampleSheet-nonSHARE-seq.config 1 -prefix zz -suffix -L003-13
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py zzUndetermined_S0_L003_R1_001.fastq.gz130 zzUndetermined_S0_L003_R1_001.fastq.gz130 | python /oak/stanford/groups/akundaje/marinovg/code/demultiplexFASTQDualIndex.py - SampleSheet-nonSHARE-seq.config 1 -prefix zz -suffix -L003-130
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py zzUndetermined_S0_L003_R1_001.fastq.gz131 zzUndetermined_S0_L003_R1_001.fastq.gz131 | python /oak/stanford/groups/akundaje/marinovg/code/demultiplexFASTQDualIndex.py - SampleSheet-nonSHARE-seq.config 1 -prefix zz -suffix -L003-131
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py zzUndetermined_S0_L003_R1_001.fastq.gz14 zzUndetermined_S0_L003_R1_001.fastq.gz14 | python /oak/stanford/groups/akundaje/marinovg/code/demultiplexFASTQDualIndex.py - SampleSheet-nonSHARE-seq.config 1 -prefix zz -suffix -L003-14
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py zzUndetermined_S0_L003_R1_001.fastq.gz15 zzUndetermined_S0_L003_R1_001.fastq.gz15 | python /oak/stanford/groups/akundaje/marinovg/code/demultiplexFASTQDualIndex.py - SampleSheet-nonSHARE-seq.config 1 -prefix zz -suffix -L003-15
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py zzUndetermined_S0_L003_R1_001.fastq.gz16 zzUndetermined_S0_L003_R1_001.fastq.gz16 | python /oak/stanford/groups/akundaje/marinovg/code/demultiplexFASTQDualIndex.py - SampleSheet-nonSHARE-seq.config 1 -prefix zz -suffix -L003-16
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py zzUndetermined_S0_L003_R1_001.fastq.gz17 zzUndetermined_S0_L003_R1_001.fastq.gz17 | python /oak/stanford/groups/akundaje/marinovg/code/demultiplexFASTQDualIndex.py - SampleSheet-nonSHARE-seq.config 1 -prefix zz -suffix -L003-17
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py zzUndetermined_S0_L003_R1_001.fastq.gz18 zzUndetermined_S0_L003_R1_001.fastq.gz18 | python /oak/stanford/groups/akundaje/marinovg/code/demultiplexFASTQDualIndex.py - SampleSheet-nonSHARE-seq.config 1 -prefix zz -suffix -L003-18
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py zzUndetermined_S0_L003_R1_001.fastq.gz19 zzUndetermined_S0_L003_R1_001.fastq.gz19 | python /oak/stanford/groups/akundaje/marinovg/code/demultiplexFASTQDualIndex.py - SampleSheet-nonSHARE-seq.config 1 -prefix zz -suffix -L003-19
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py zzUndetermined_S0_L003_R1_001.fastq.gz2 zzUndetermined_S0_L003_R1_001.fastq.gz2 | python /oak/stanford/groups/akundaje/marinovg/code/demultiplexFASTQDualIndex.py - SampleSheet-nonSHARE-seq.config 1 -prefix zz -suffix -L003-2
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py zzUndetermined_S0_L003_R1_001.fastq.gz20 zzUndetermined_S0_L003_R1_001.fastq.gz20 | python /oak/stanford/groups/akundaje/marinovg/code/demultiplexFASTQDualIndex.py - SampleSheet-nonSHARE-seq.config 1 -prefix zz -suffix -L003-20
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py zzUndetermined_S0_L003_R1_001.fastq.gz21 zzUndetermined_S0_L003_R1_001.fastq.gz21 | python /oak/stanford/groups/akundaje/marinovg/code/demultiplexFASTQDualIndex.py - SampleSheet-nonSHARE-seq.config 1 -prefix zz -suffix -L003-21
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py zzUndetermined_S0_L003_R1_001.fastq.gz22 zzUndetermined_S0_L003_R1_001.fastq.gz22 | python /oak/stanford/groups/akundaje/marinovg/code/demultiplexFASTQDualIndex.py - SampleSheet-nonSHARE-seq.config 1 -prefix zz -suffix -L003-22
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py zzUndetermined_S0_L003_R1_001.fastq.gz23 zzUndetermined_S0_L003_R1_001.fastq.gz23 | python /oak/stanford/groups/akundaje/marinovg/code/demultiplexFASTQDualIndex.py - SampleSheet-nonSHARE-seq.config 1 -prefix zz -suffix -L003-23
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py zzUndetermined_S0_L003_R1_001.fastq.gz24 zzUndetermined_S0_L003_R1_001.fastq.gz24 | python /oak/stanford/groups/akundaje/marinovg/code/demultiplexFASTQDualIndex.py - SampleSheet-nonSHARE-seq.config 1 -prefix zz -suffix -L003-24
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py zzUndetermined_S0_L003_R1_001.fastq.gz25 zzUndetermined_S0_L003_R1_001.fastq.gz25 | python /oak/stanford/groups/akundaje/marinovg/code/demultiplexFASTQDualIndex.py - SampleSheet-nonSHARE-seq.config 1 -prefix zz -suffix -L003-25
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py zzUndetermined_S0_L003_R1_001.fastq.gz26 zzUndetermined_S0_L003_R1_001.fastq.gz26 | python /oak/stanford/groups/akundaje/marinovg/code/demultiplexFASTQDualIndex.py - SampleSheet-nonSHARE-seq.config 1 -prefix zz -suffix -L003-26
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py zzUndetermined_S0_L003_R1_001.fastq.gz27 zzUndetermined_S0_L003_R1_001.fastq.gz27 | python /oak/stanford/groups/akundaje/marinovg/code/demultiplexFASTQDualIndex.py - SampleSheet-nonSHARE-seq.config 1 -prefix zz -suffix -L003-27
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py zzUndetermined_S0_L003_R1_001.fastq.gz28 zzUndetermined_S0_L003_R1_001.fastq.gz28 | python /oak/stanford/groups/akundaje/marinovg/code/demultiplexFASTQDualIndex.py - SampleSheet-nonSHARE-seq.config 1 -prefix zz -suffix -L003-28
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py zzUndetermined_S0_L003_R1_001.fastq.gz29 zzUndetermined_S0_L003_R1_001.fastq.gz29 | python /oak/stanford/groups/akundaje/marinovg/code/demultiplexFASTQDualIndex.py - SampleSheet-nonSHARE-seq.config 1 -prefix zz -suffix -L003-29
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py zzUndetermined_S0_L003_R1_001.fastq.gz3 zzUndetermined_S0_L003_R1_001.fastq.gz3 | python /oak/stanford/groups/akundaje/marinovg/code/demultiplexFASTQDualIndex.py - SampleSheet-nonSHARE-seq.config 1 -prefix zz -suffix -L003-3
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py zzUndetermined_S0_L003_R1_001.fastq.gz30 zzUndetermined_S0_L003_R1_001.fastq.gz30 | python /oak/stanford/groups/akundaje/marinovg/code/demultiplexFASTQDualIndex.py - SampleSheet-nonSHARE-seq.config 1 -prefix zz -suffix -L003-30
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py zzUndetermined_S0_L003_R1_001.fastq.gz31 zzUndetermined_S0_L003_R1_001.fastq.gz31 | python /oak/stanford/groups/akundaje/marinovg/code/demultiplexFASTQDualIndex.py - SampleSheet-nonSHARE-seq.config 1 -prefix zz -suffix -L003-31
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py zzUndetermined_S0_L003_R1_001.fastq.gz32 zzUndetermined_S0_L003_R1_001.fastq.gz32 | python /oak/stanford/groups/akundaje/marinovg/code/demultiplexFASTQDualIndex.py - SampleSheet-nonSHARE-seq.config 1 -prefix zz -suffix -L003-32
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py zzUndetermined_S0_L003_R1_001.fastq.gz33 zzUndetermined_S0_L003_R1_001.fastq.gz33 | python /oak/stanford/groups/akundaje/marinovg/code/demultiplexFASTQDualIndex.py - SampleSheet-nonSHARE-seq.config 1 -prefix zz -suffix -L003-33
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py zzUndetermined_S0_L003_R1_001.fastq.gz34 zzUndetermined_S0_L003_R1_001.fastq.gz34 | python /oak/stanford/groups/akundaje/marinovg/code/demultiplexFASTQDualIndex.py - SampleSheet-nonSHARE-seq.config 1 -prefix zz -suffix -L003-34
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py zzUndetermined_S0_L003_R1_001.fastq.gz35 zzUndetermined_S0_L003_R1_001.fastq.gz35 | python /oak/stanford/groups/akundaje/marinovg/code/demultiplexFASTQDualIndex.py - SampleSheet-nonSHARE-seq.config 1 -prefix zz -suffix -L003-35
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py zzUndetermined_S0_L003_R1_001.fastq.gz36 zzUndetermined_S0_L003_R1_001.fastq.gz36 | python /oak/stanford/groups/akundaje/marinovg/code/demultiplexFASTQDualIndex.py - SampleSheet-nonSHARE-seq.config 1 -prefix zz -suffix -L003-36
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py zzUndetermined_S0_L003_R1_001.fastq.gz37 zzUndetermined_S0_L003_R1_001.fastq.gz37 | python /oak/stanford/groups/akundaje/marinovg/code/demultiplexFASTQDualIndex.py - SampleSheet-nonSHARE-seq.config 1 -prefix zz -suffix -L003-37
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py zzUndetermined_S0_L003_R1_001.fastq.gz38 zzUndetermined_S0_L003_R1_001.fastq.gz38 | python /oak/stanford/groups/akundaje/marinovg/code/demultiplexFASTQDualIndex.py - SampleSheet-nonSHARE-seq.config 1 -prefix zz -suffix -L003-38
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py zzUndetermined_S0_L003_R1_001.fastq.gz39 zzUndetermined_S0_L003_R1_001.fastq.gz39 | python /oak/stanford/groups/akundaje/marinovg/code/demultiplexFASTQDualIndex.py - SampleSheet-nonSHARE-seq.config 1 -prefix zz -suffix -L003-39
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py zzUndetermined_S0_L003_R1_001.fastq.gz4 zzUndetermined_S0_L003_R1_001.fastq.gz4 | python /oak/stanford/groups/akundaje/marinovg/code/demultiplexFASTQDualIndex.py - SampleSheet-nonSHARE-seq.config 1 -prefix zz -suffix -L003-4
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py zzUndetermined_S0_L003_R1_001.fastq.gz40 zzUndetermined_S0_L003_R1_001.fastq.gz40 | python /oak/stanford/groups/akundaje/marinovg/code/demultiplexFASTQDualIndex.py - SampleSheet-nonSHARE-seq.config 1 -prefix zz -suffix -L003-40
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py zzUndetermined_S0_L003_R1_001.fastq.gz41 zzUndetermined_S0_L003_R1_001.fastq.gz41 | python /oak/stanford/groups/akundaje/marinovg/code/demultiplexFASTQDualIndex.py - SampleSheet-nonSHARE-seq.config 1 -prefix zz -suffix -L003-41
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py zzUndetermined_S0_L003_R1_001.fastq.gz42 zzUndetermined_S0_L003_R1_001.fastq.gz42 | python /oak/stanford/groups/akundaje/marinovg/code/demultiplexFASTQDualIndex.py - SampleSheet-nonSHARE-seq.config 1 -prefix zz -suffix -L003-42
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py zzUndetermined_S0_L003_R1_001.fastq.gz43 zzUndetermined_S0_L003_R1_001.fastq.gz43 | python /oak/stanford/groups/akundaje/marinovg/code/demultiplexFASTQDualIndex.py - SampleSheet-nonSHARE-seq.config 1 -prefix zz -suffix -L003-43
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py zzUndetermined_S0_L003_R1_001.fastq.gz44 zzUndetermined_S0_L003_R1_001.fastq.gz44 | python /oak/stanford/groups/akundaje/marinovg/code/demultiplexFASTQDualIndex.py - SampleSheet-nonSHARE-seq.config 1 -prefix zz -suffix -L003-44
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py zzUndetermined_S0_L003_R1_001.fastq.gz45 zzUndetermined_S0_L003_R1_001.fastq.gz45 | python /oak/stanford/groups/akundaje/marinovg/code/demultiplexFASTQDualIndex.py - SampleSheet-nonSHARE-seq.config 1 -prefix zz -suffix -L003-45
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py zzUndetermined_S0_L003_R1_001.fastq.gz46 zzUndetermined_S0_L003_R1_001.fastq.gz46 | python /oak/stanford/groups/akundaje/marinovg/code/demultiplexFASTQDualIndex.py - SampleSheet-nonSHARE-seq.config 1 -prefix zz -suffix -L003-46
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py zzUndetermined_S0_L003_R1_001.fastq.gz47 zzUndetermined_S0_L003_R1_001.fastq.gz47 | python /oak/stanford/groups/akundaje/marinovg/code/demultiplexFASTQDualIndex.py - SampleSheet-nonSHARE-seq.config 1 -prefix zz -suffix -L003-47
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py zzUndetermined_S0_L003_R1_001.fastq.gz48 zzUndetermined_S0_L003_R1_001.fastq.gz48 | python /oak/stanford/groups/akundaje/marinovg/code/demultiplexFASTQDualIndex.py - SampleSheet-nonSHARE-seq.config 1 -prefix zz -suffix -L003-48
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py zzUndetermined_S0_L003_R1_001.fastq.gz49 zzUndetermined_S0_L003_R1_001.fastq.gz49 | python /oak/stanford/groups/akundaje/marinovg/code/demultiplexFASTQDualIndex.py - SampleSheet-nonSHARE-seq.config 1 -prefix zz -suffix -L003-49
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py zzUndetermined_S0_L003_R1_001.fastq.gz5 zzUndetermined_S0_L003_R1_001.fastq.gz5 | python /oak/stanford/groups/akundaje/marinovg/code/demultiplexFASTQDualIndex.py - SampleSheet-nonSHARE-seq.config 1 -prefix zz -suffix -L003-5
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py zzUndetermined_S0_L003_R1_001.fastq.gz50 zzUndetermined_S0_L003_R1_001.fastq.gz50 | python /oak/stanford/groups/akundaje/marinovg/code/demultiplexFASTQDualIndex.py - SampleSheet-nonSHARE-seq.config 1 -prefix zz -suffix -L003-50
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py zzUndetermined_S0_L003_R1_001.fastq.gz51 zzUndetermined_S0_L003_R1_001.fastq.gz51 | python /oak/stanford/groups/akundaje/marinovg/code/demultiplexFASTQDualIndex.py - SampleSheet-nonSHARE-seq.config 1 -prefix zz -suffix -L003-51
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py zzUndetermined_S0_L003_R1_001.fastq.gz52 zzUndetermined_S0_L003_R1_001.fastq.gz52 | python /oak/stanford/groups/akundaje/marinovg/code/demultiplexFASTQDualIndex.py - SampleSheet-nonSHARE-seq.config 1 -prefix zz -suffix -L003-52
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py zzUndetermined_S0_L003_R1_001.fastq.gz53 zzUndetermined_S0_L003_R1_001.fastq.gz53 | python /oak/stanford/groups/akundaje/marinovg/code/demultiplexFASTQDualIndex.py - SampleSheet-nonSHARE-seq.config 1 -prefix zz -suffix -L003-53
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py zzUndetermined_S0_L003_R1_001.fastq.gz54 zzUndetermined_S0_L003_R1_001.fastq.gz54 | python /oak/stanford/groups/akundaje/marinovg/code/demultiplexFASTQDualIndex.py - SampleSheet-nonSHARE-seq.config 1 -prefix zz -suffix -L003-54
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py zzUndetermined_S0_L003_R1_001.fastq.gz55 zzUndetermined_S0_L003_R1_001.fastq.gz55 | python /oak/stanford/groups/akundaje/marinovg/code/demultiplexFASTQDualIndex.py - SampleSheet-nonSHARE-seq.config 1 -prefix zz -suffix -L003-55
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py zzUndetermined_S0_L003_R1_001.fastq.gz56 zzUndetermined_S0_L003_R1_001.fastq.gz56 | python /oak/stanford/groups/akundaje/marinovg/code/demultiplexFASTQDualIndex.py - SampleSheet-nonSHARE-seq.config 1 -prefix zz -suffix -L003-56
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py zzUndetermined_S0_L003_R1_001.fastq.gz57 zzUndetermined_S0_L003_R1_001.fastq.gz57 | python /oak/stanford/groups/akundaje/marinovg/code/demultiplexFASTQDualIndex.py - SampleSheet-nonSHARE-seq.config 1 -prefix zz -suffix -L003-57
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py zzUndetermined_S0_L003_R1_001.fastq.gz58 zzUndetermined_S0_L003_R1_001.fastq.gz58 | python /oak/stanford/groups/akundaje/marinovg/code/demultiplexFASTQDualIndex.py - SampleSheet-nonSHARE-seq.config 1 -prefix zz -suffix -L003-58
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py zzUndetermined_S0_L003_R1_001.fastq.gz59 zzUndetermined_S0_L003_R1_001.fastq.gz59 | python /oak/stanford/groups/akundaje/marinovg/code/demultiplexFASTQDualIndex.py - SampleSheet-nonSHARE-seq.config 1 -prefix zz -suffix -L003-59
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py zzUndetermined_S0_L003_R1_001.fastq.gz6 zzUndetermined_S0_L003_R1_001.fastq.gz6 | python /oak/stanford/groups/akundaje/marinovg/code/demultiplexFASTQDualIndex.py - SampleSheet-nonSHARE-seq.config 1 -prefix zz -suffix -L003-6
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py zzUndetermined_S0_L003_R1_001.fastq.gz60 zzUndetermined_S0_L003_R1_001.fastq.gz60 | python /oak/stanford/groups/akundaje/marinovg/code/demultiplexFASTQDualIndex.py - SampleSheet-nonSHARE-seq.config 1 -prefix zz -suffix -L003-60
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py zzUndetermined_S0_L003_R1_001.fastq.gz61 zzUndetermined_S0_L003_R1_001.fastq.gz61 | python /oak/stanford/groups/akundaje/marinovg/code/demultiplexFASTQDualIndex.py - SampleSheet-nonSHARE-seq.config 1 -prefix zz -suffix -L003-61
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py zzUndetermined_S0_L003_R1_001.fastq.gz62 zzUndetermined_S0_L003_R1_001.fastq.gz62 | python /oak/stanford/groups/akundaje/marinovg/code/demultiplexFASTQDualIndex.py - SampleSheet-nonSHARE-seq.config 1 -prefix zz -suffix -L003-62
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py zzUndetermined_S0_L003_R1_001.fastq.gz63 zzUndetermined_S0_L003_R1_001.fastq.gz63 | python /oak/stanford/groups/akundaje/marinovg/code/demultiplexFASTQDualIndex.py - SampleSheet-nonSHARE-seq.config 1 -prefix zz -suffix -L003-63
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py zzUndetermined_S0_L003_R1_001.fastq.gz64 zzUndetermined_S0_L003_R1_001.fastq.gz64 | python /oak/stanford/groups/akundaje/marinovg/code/demultiplexFASTQDualIndex.py - SampleSheet-nonSHARE-seq.config 1 -prefix zz -suffix -L003-64
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py zzUndetermined_S0_L003_R1_001.fastq.gz65 zzUndetermined_S0_L003_R1_001.fastq.gz65 | python /oak/stanford/groups/akundaje/marinovg/code/demultiplexFASTQDualIndex.py - SampleSheet-nonSHARE-seq.config 1 -prefix zz -suffix -L003-65
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py zzUndetermined_S0_L003_R1_001.fastq.gz66 zzUndetermined_S0_L003_R1_001.fastq.gz66 | python /oak/stanford/groups/akundaje/marinovg/code/demultiplexFASTQDualIndex.py - SampleSheet-nonSHARE-seq.config 1 -prefix zz -suffix -L003-66
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py zzUndetermined_S0_L003_R1_001.fastq.gz67 zzUndetermined_S0_L003_R1_001.fastq.gz67 | python /oak/stanford/groups/akundaje/marinovg/code/demultiplexFASTQDualIndex.py - SampleSheet-nonSHARE-seq.config 1 -prefix zz -suffix -L003-67
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py zzUndetermined_S0_L003_R1_001.fastq.gz68 zzUndetermined_S0_L003_R1_001.fastq.gz68 | python /oak/stanford/groups/akundaje/marinovg/code/demultiplexFASTQDualIndex.py - SampleSheet-nonSHARE-seq.config 1 -prefix zz -suffix -L003-68
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py zzUndetermined_S0_L003_R1_001.fastq.gz69 zzUndetermined_S0_L003_R1_001.fastq.gz69 | python /oak/stanford/groups/akundaje/marinovg/code/demultiplexFASTQDualIndex.py - SampleSheet-nonSHARE-seq.config 1 -prefix zz -suffix -L003-69
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py zzUndetermined_S0_L003_R1_001.fastq.gz7 zzUndetermined_S0_L003_R1_001.fastq.gz7 | python /oak/stanford/groups/akundaje/marinovg/code/demultiplexFASTQDualIndex.py - SampleSheet-nonSHARE-seq.config 1 -prefix zz -suffix -L003-7
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py zzUndetermined_S0_L003_R1_001.fastq.gz70 zzUndetermined_S0_L003_R1_001.fastq.gz70 | python /oak/stanford/groups/akundaje/marinovg/code/demultiplexFASTQDualIndex.py - SampleSheet-nonSHARE-seq.config 1 -prefix zz -suffix -L003-70
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py zzUndetermined_S0_L003_R1_001.fastq.gz71 zzUndetermined_S0_L003_R1_001.fastq.gz71 | python /oak/stanford/groups/akundaje/marinovg/code/demultiplexFASTQDualIndex.py - SampleSheet-nonSHARE-seq.config 1 -prefix zz -suffix -L003-71
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py zzUndetermined_S0_L003_R1_001.fastq.gz72 zzUndetermined_S0_L003_R1_001.fastq.gz72 | python /oak/stanford/groups/akundaje/marinovg/code/demultiplexFASTQDualIndex.py - SampleSheet-nonSHARE-seq.config 1 -prefix zz -suffix -L003-72
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py zzUndetermined_S0_L003_R1_001.fastq.gz73 zzUndetermined_S0_L003_R1_001.fastq.gz73 | python /oak/stanford/groups/akundaje/marinovg/code/demultiplexFASTQDualIndex.py - SampleSheet-nonSHARE-seq.config 1 -prefix zz -suffix -L003-73
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py zzUndetermined_S0_L003_R1_001.fastq.gz74 zzUndetermined_S0_L003_R1_001.fastq.gz74 | python /oak/stanford/groups/akundaje/marinovg/code/demultiplexFASTQDualIndex.py - SampleSheet-nonSHARE-seq.config 1 -prefix zz -suffix -L003-74
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py zzUndetermined_S0_L003_R1_001.fastq.gz75 zzUndetermined_S0_L003_R1_001.fastq.gz75 | python /oak/stanford/groups/akundaje/marinovg/code/demultiplexFASTQDualIndex.py - SampleSheet-nonSHARE-seq.config 1 -prefix zz -suffix -L003-75
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py zzUndetermined_S0_L003_R1_001.fastq.gz76 zzUndetermined_S0_L003_R1_001.fastq.gz76 | python /oak/stanford/groups/akundaje/marinovg/code/demultiplexFASTQDualIndex.py - SampleSheet-nonSHARE-seq.config 1 -prefix zz -suffix -L003-76
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py zzUndetermined_S0_L003_R1_001.fastq.gz77 zzUndetermined_S0_L003_R1_001.fastq.gz77 | python /oak/stanford/groups/akundaje/marinovg/code/demultiplexFASTQDualIndex.py - SampleSheet-nonSHARE-seq.config 1 -prefix zz -suffix -L003-77
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py zzUndetermined_S0_L003_R1_001.fastq.gz78 zzUndetermined_S0_L003_R1_001.fastq.gz78 | python /oak/stanford/groups/akundaje/marinovg/code/demultiplexFASTQDualIndex.py - SampleSheet-nonSHARE-seq.config 1 -prefix zz -suffix -L003-78
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py zzUndetermined_S0_L003_R1_001.fastq.gz79 zzUndetermined_S0_L003_R1_001.fastq.gz79 | python /oak/stanford/groups/akundaje/marinovg/code/demultiplexFASTQDualIndex.py - SampleSheet-nonSHARE-seq.config 1 -prefix zz -suffix -L003-79
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py zzUndetermined_S0_L003_R1_001.fastq.gz8 zzUndetermined_S0_L003_R1_001.fastq.gz8 | python /oak/stanford/groups/akundaje/marinovg/code/demultiplexFASTQDualIndex.py - SampleSheet-nonSHARE-seq.config 1 -prefix zz -suffix -L003-8
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py zzUndetermined_S0_L003_R1_001.fastq.gz80 zzUndetermined_S0_L003_R1_001.fastq.gz80 | python /oak/stanford/groups/akundaje/marinovg/code/demultiplexFASTQDualIndex.py - SampleSheet-nonSHARE-seq.config 1 -prefix zz -suffix -L003-80
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py zzUndetermined_S0_L003_R1_001.fastq.gz81 zzUndetermined_S0_L003_R1_001.fastq.gz81 | python /oak/stanford/groups/akundaje/marinovg/code/demultiplexFASTQDualIndex.py - SampleSheet-nonSHARE-seq.config 1 -prefix zz -suffix -L003-81
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py zzUndetermined_S0_L003_R1_001.fastq.gz82 zzUndetermined_S0_L003_R1_001.fastq.gz82 | python /oak/stanford/groups/akundaje/marinovg/code/demultiplexFASTQDualIndex.py - SampleSheet-nonSHARE-seq.config 1 -prefix zz -suffix -L003-82
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py zzUndetermined_S0_L003_R1_001.fastq.gz83 zzUndetermined_S0_L003_R1_001.fastq.gz83 | python /oak/stanford/groups/akundaje/marinovg/code/demultiplexFASTQDualIndex.py - SampleSheet-nonSHARE-seq.config 1 -prefix zz -suffix -L003-83
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py zzUndetermined_S0_L003_R1_001.fastq.gz84 zzUndetermined_S0_L003_R1_001.fastq.gz84 | python /oak/stanford/groups/akundaje/marinovg/code/demultiplexFASTQDualIndex.py - SampleSheet-nonSHARE-seq.config 1 -prefix zz -suffix -L003-84
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py zzUndetermined_S0_L003_R1_001.fastq.gz85 zzUndetermined_S0_L003_R1_001.fastq.gz85 | python /oak/stanford/groups/akundaje/marinovg/code/demultiplexFASTQDualIndex.py - SampleSheet-nonSHARE-seq.config 1 -prefix zz -suffix -L003-85
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py zzUndetermined_S0_L003_R1_001.fastq.gz86 zzUndetermined_S0_L003_R1_001.fastq.gz86 | python /oak/stanford/groups/akundaje/marinovg/code/demultiplexFASTQDualIndex.py - SampleSheet-nonSHARE-seq.config 1 -prefix zz -suffix -L003-86
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py zzUndetermined_S0_L003_R1_001.fastq.gz87 zzUndetermined_S0_L003_R1_001.fastq.gz87 | python /oak/stanford/groups/akundaje/marinovg/code/demultiplexFASTQDualIndex.py - SampleSheet-nonSHARE-seq.config 1 -prefix zz -suffix -L003-87
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py zzUndetermined_S0_L003_R1_001.fastq.gz88 zzUndetermined_S0_L003_R1_001.fastq.gz88 | python /oak/stanford/groups/akundaje/marinovg/code/demultiplexFASTQDualIndex.py - SampleSheet-nonSHARE-seq.config 1 -prefix zz -suffix -L003-88
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py zzUndetermined_S0_L003_R1_001.fastq.gz89 zzUndetermined_S0_L003_R1_001.fastq.gz89 | python /oak/stanford/groups/akundaje/marinovg/code/demultiplexFASTQDualIndex.py - SampleSheet-nonSHARE-seq.config 1 -prefix zz -suffix -L003-89
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py zzUndetermined_S0_L003_R1_001.fastq.gz9 zzUndetermined_S0_L003_R1_001.fastq.gz9 | python /oak/stanford/groups/akundaje/marinovg/code/demultiplexFASTQDualIndex.py - SampleSheet-nonSHARE-seq.config 1 -prefix zz -suffix -L003-9
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py zzUndetermined_S0_L003_R1_001.fastq.gz90 zzUndetermined_S0_L003_R1_001.fastq.gz90 | python /oak/stanford/groups/akundaje/marinovg/code/demultiplexFASTQDualIndex.py - SampleSheet-nonSHARE-seq.config 1 -prefix zz -suffix -L003-90
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py zzUndetermined_S0_L003_R1_001.fastq.gz91 zzUndetermined_S0_L003_R1_001.fastq.gz91 | python /oak/stanford/groups/akundaje/marinovg/code/demultiplexFASTQDualIndex.py - SampleSheet-nonSHARE-seq.config 1 -prefix zz -suffix -L003-91
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py zzUndetermined_S0_L003_R1_001.fastq.gz92 zzUndetermined_S0_L003_R1_001.fastq.gz92 | python /oak/stanford/groups/akundaje/marinovg/code/demultiplexFASTQDualIndex.py - SampleSheet-nonSHARE-seq.config 1 -prefix zz -suffix -L003-92
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py zzUndetermined_S0_L003_R1_001.fastq.gz93 zzUndetermined_S0_L003_R1_001.fastq.gz93 | python /oak/stanford/groups/akundaje/marinovg/code/demultiplexFASTQDualIndex.py - SampleSheet-nonSHARE-seq.config 1 -prefix zz -suffix -L003-93
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py zzUndetermined_S0_L003_R1_001.fastq.gz94 zzUndetermined_S0_L003_R1_001.fastq.gz94 | python /oak/stanford/groups/akundaje/marinovg/code/demultiplexFASTQDualIndex.py - SampleSheet-nonSHARE-seq.config 1 -prefix zz -suffix -L003-94
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py zzUndetermined_S0_L003_R1_001.fastq.gz95 zzUndetermined_S0_L003_R1_001.fastq.gz95 | python /oak/stanford/groups/akundaje/marinovg/code/demultiplexFASTQDualIndex.py - SampleSheet-nonSHARE-seq.config 1 -prefix zz -suffix -L003-95
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py zzUndetermined_S0_L003_R1_001.fastq.gz96 zzUndetermined_S0_L003_R1_001.fastq.gz96 | python /oak/stanford/groups/akundaje/marinovg/code/demultiplexFASTQDualIndex.py - SampleSheet-nonSHARE-seq.config 1 -prefix zz -suffix -L003-96
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py zzUndetermined_S0_L003_R1_001.fastq.gz97 zzUndetermined_S0_L003_R1_001.fastq.gz97 | python /oak/stanford/groups/akundaje/marinovg/code/demultiplexFASTQDualIndex.py - SampleSheet-nonSHARE-seq.config 1 -prefix zz -suffix -L003-97
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py zzUndetermined_S0_L003_R1_001.fastq.gz98 zzUndetermined_S0_L003_R1_001.fastq.gz98 | python /oak/stanford/groups/akundaje/marinovg/code/demultiplexFASTQDualIndex.py - SampleSheet-nonSHARE-seq.config 1 -prefix zz -suffix -L003-98
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py zzUndetermined_S0_L003_R1_001.fastq.gz99 zzUndetermined_S0_L003_R1_001.fastq.gz99 | python /oak/stanford/groups/akundaje/marinovg/code/demultiplexFASTQDualIndex.py - SampleSheet-nonSHARE-seq.config 1 -prefix zz -suffix -L003-99
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py zzUndetermined_S0_L004_R1_001.fastq.gz0 zzUndetermined_S0_L004_R1_001.fastq.gz0 | python /oak/stanford/groups/akundaje/marinovg/code/demultiplexFASTQDualIndex.py - SampleSheet-nonSHARE-seq.config 1 -prefix zz -suffix -L004-0
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py zzUndetermined_S0_L004_R1_001.fastq.gz1 zzUndetermined_S0_L004_R1_001.fastq.gz1 | python /oak/stanford/groups/akundaje/marinovg/code/demultiplexFASTQDualIndex.py - SampleSheet-nonSHARE-seq.config 1 -prefix zz -suffix -L004-1
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py zzUndetermined_S0_L004_R1_001.fastq.gz10 zzUndetermined_S0_L004_R1_001.fastq.gz10 | python /oak/stanford/groups/akundaje/marinovg/code/demultiplexFASTQDualIndex.py - SampleSheet-nonSHARE-seq.config 1 -prefix zz -suffix -L004-10
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py zzUndetermined_S0_L004_R1_001.fastq.gz100 zzUndetermined_S0_L004_R1_001.fastq.gz100 | python /oak/stanford/groups/akundaje/marinovg/code/demultiplexFASTQDualIndex.py - SampleSheet-nonSHARE-seq.config 1 -prefix zz -suffix -L004-100
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py zzUndetermined_S0_L004_R1_001.fastq.gz101 zzUndetermined_S0_L004_R1_001.fastq.gz101 | python /oak/stanford/groups/akundaje/marinovg/code/demultiplexFASTQDualIndex.py - SampleSheet-nonSHARE-seq.config 1 -prefix zz -suffix -L004-101
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py zzUndetermined_S0_L004_R1_001.fastq.gz102 zzUndetermined_S0_L004_R1_001.fastq.gz102 | python /oak/stanford/groups/akundaje/marinovg/code/demultiplexFASTQDualIndex.py - SampleSheet-nonSHARE-seq.config 1 -prefix zz -suffix -L004-102
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py zzUndetermined_S0_L004_R1_001.fastq.gz103 zzUndetermined_S0_L004_R1_001.fastq.gz103 | python /oak/stanford/groups/akundaje/marinovg/code/demultiplexFASTQDualIndex.py - SampleSheet-nonSHARE-seq.config 1 -prefix zz -suffix -L004-103
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py zzUndetermined_S0_L004_R1_001.fastq.gz104 zzUndetermined_S0_L004_R1_001.fastq.gz104 | python /oak/stanford/groups/akundaje/marinovg/code/demultiplexFASTQDualIndex.py - SampleSheet-nonSHARE-seq.config 1 -prefix zz -suffix -L004-104
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py zzUndetermined_S0_L004_R1_001.fastq.gz105 zzUndetermined_S0_L004_R1_001.fastq.gz105 | python /oak/stanford/groups/akundaje/marinovg/code/demultiplexFASTQDualIndex.py - SampleSheet-nonSHARE-seq.config 1 -prefix zz -suffix -L004-105
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py zzUndetermined_S0_L004_R1_001.fastq.gz106 zzUndetermined_S0_L004_R1_001.fastq.gz106 | python /oak/stanford/groups/akundaje/marinovg/code/demultiplexFASTQDualIndex.py - SampleSheet-nonSHARE-seq.config 1 -prefix zz -suffix -L004-106
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py zzUndetermined_S0_L004_R1_001.fastq.gz107 zzUndetermined_S0_L004_R1_001.fastq.gz107 | python /oak/stanford/groups/akundaje/marinovg/code/demultiplexFASTQDualIndex.py - SampleSheet-nonSHARE-seq.config 1 -prefix zz -suffix -L004-107
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py zzUndetermined_S0_L004_R1_001.fastq.gz108 zzUndetermined_S0_L004_R1_001.fastq.gz108 | python /oak/stanford/groups/akundaje/marinovg/code/demultiplexFASTQDualIndex.py - SampleSheet-nonSHARE-seq.config 1 -prefix zz -suffix -L004-108
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py zzUndetermined_S0_L004_R1_001.fastq.gz109 zzUndetermined_S0_L004_R1_001.fastq.gz109 | python /oak/stanford/groups/akundaje/marinovg/code/demultiplexFASTQDualIndex.py - SampleSheet-nonSHARE-seq.config 1 -prefix zz -suffix -L004-109
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py zzUndetermined_S0_L004_R1_001.fastq.gz11 zzUndetermined_S0_L004_R1_001.fastq.gz11 | python /oak/stanford/groups/akundaje/marinovg/code/demultiplexFASTQDualIndex.py - SampleSheet-nonSHARE-seq.config 1 -prefix zz -suffix -L004-11
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py zzUndetermined_S0_L004_R1_001.fastq.gz110 zzUndetermined_S0_L004_R1_001.fastq.gz110 | python /oak/stanford/groups/akundaje/marinovg/code/demultiplexFASTQDualIndex.py - SampleSheet-nonSHARE-seq.config 1 -prefix zz -suffix -L004-110
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py zzUndetermined_S0_L004_R1_001.fastq.gz111 zzUndetermined_S0_L004_R1_001.fastq.gz111 | python /oak/stanford/groups/akundaje/marinovg/code/demultiplexFASTQDualIndex.py - SampleSheet-nonSHARE-seq.config 1 -prefix zz -suffix -L004-111
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py zzUndetermined_S0_L004_R1_001.fastq.gz112 zzUndetermined_S0_L004_R1_001.fastq.gz112 | python /oak/stanford/groups/akundaje/marinovg/code/demultiplexFASTQDualIndex.py - SampleSheet-nonSHARE-seq.config 1 -prefix zz -suffix -L004-112
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py zzUndetermined_S0_L004_R1_001.fastq.gz113 zzUndetermined_S0_L004_R1_001.fastq.gz113 | python /oak/stanford/groups/akundaje/marinovg/code/demultiplexFASTQDualIndex.py - SampleSheet-nonSHARE-seq.config 1 -prefix zz -suffix -L004-113
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py zzUndetermined_S0_L004_R1_001.fastq.gz114 zzUndetermined_S0_L004_R1_001.fastq.gz114 | python /oak/stanford/groups/akundaje/marinovg/code/demultiplexFASTQDualIndex.py - SampleSheet-nonSHARE-seq.config 1 -prefix zz -suffix -L004-114
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py zzUndetermined_S0_L004_R1_001.fastq.gz115 zzUndetermined_S0_L004_R1_001.fastq.gz115 | python /oak/stanford/groups/akundaje/marinovg/code/demultiplexFASTQDualIndex.py - SampleSheet-nonSHARE-seq.config 1 -prefix zz -suffix -L004-115
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py zzUndetermined_S0_L004_R1_001.fastq.gz116 zzUndetermined_S0_L004_R1_001.fastq.gz116 | python /oak/stanford/groups/akundaje/marinovg/code/demultiplexFASTQDualIndex.py - SampleSheet-nonSHARE-seq.config 1 -prefix zz -suffix -L004-116
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py zzUndetermined_S0_L004_R1_001.fastq.gz117 zzUndetermined_S0_L004_R1_001.fastq.gz117 | python /oak/stanford/groups/akundaje/marinovg/code/demultiplexFASTQDualIndex.py - SampleSheet-nonSHARE-seq.config 1 -prefix zz -suffix -L004-117
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py zzUndetermined_S0_L004_R1_001.fastq.gz118 zzUndetermined_S0_L004_R1_001.fastq.gz118 | python /oak/stanford/groups/akundaje/marinovg/code/demultiplexFASTQDualIndex.py - SampleSheet-nonSHARE-seq.config 1 -prefix zz -suffix -L004-118
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py zzUndetermined_S0_L004_R1_001.fastq.gz119 zzUndetermined_S0_L004_R1_001.fastq.gz119 | python /oak/stanford/groups/akundaje/marinovg/code/demultiplexFASTQDualIndex.py - SampleSheet-nonSHARE-seq.config 1 -prefix zz -suffix -L004-119
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py zzUndetermined_S0_L004_R1_001.fastq.gz12 zzUndetermined_S0_L004_R1_001.fastq.gz12 | python /oak/stanford/groups/akundaje/marinovg/code/demultiplexFASTQDualIndex.py - SampleSheet-nonSHARE-seq.config 1 -prefix zz -suffix -L004-12
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py zzUndetermined_S0_L004_R1_001.fastq.gz120 zzUndetermined_S0_L004_R1_001.fastq.gz120 | python /oak/stanford/groups/akundaje/marinovg/code/demultiplexFASTQDualIndex.py - SampleSheet-nonSHARE-seq.config 1 -prefix zz -suffix -L004-120
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py zzUndetermined_S0_L004_R1_001.fastq.gz121 zzUndetermined_S0_L004_R1_001.fastq.gz121 | python /oak/stanford/groups/akundaje/marinovg/code/demultiplexFASTQDualIndex.py - SampleSheet-nonSHARE-seq.config 1 -prefix zz -suffix -L004-121
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py zzUndetermined_S0_L004_R1_001.fastq.gz122 zzUndetermined_S0_L004_R1_001.fastq.gz122 | python /oak/stanford/groups/akundaje/marinovg/code/demultiplexFASTQDualIndex.py - SampleSheet-nonSHARE-seq.config 1 -prefix zz -suffix -L004-122
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py zzUndetermined_S0_L004_R1_001.fastq.gz123 zzUndetermined_S0_L004_R1_001.fastq.gz123 | python /oak/stanford/groups/akundaje/marinovg/code/demultiplexFASTQDualIndex.py - SampleSheet-nonSHARE-seq.config 1 -prefix zz -suffix -L004-123
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py zzUndetermined_S0_L004_R1_001.fastq.gz124 zzUndetermined_S0_L004_R1_001.fastq.gz124 | python /oak/stanford/groups/akundaje/marinovg/code/demultiplexFASTQDualIndex.py - SampleSheet-nonSHARE-seq.config 1 -prefix zz -suffix -L004-124
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py zzUndetermined_S0_L004_R1_001.fastq.gz125 zzUndetermined_S0_L004_R1_001.fastq.gz125 | python /oak/stanford/groups/akundaje/marinovg/code/demultiplexFASTQDualIndex.py - SampleSheet-nonSHARE-seq.config 1 -prefix zz -suffix -L004-125
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py zzUndetermined_S0_L004_R1_001.fastq.gz126 zzUndetermined_S0_L004_R1_001.fastq.gz126 | python /oak/stanford/groups/akundaje/marinovg/code/demultiplexFASTQDualIndex.py - SampleSheet-nonSHARE-seq.config 1 -prefix zz -suffix -L004-126
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py zzUndetermined_S0_L004_R1_001.fastq.gz127 zzUndetermined_S0_L004_R1_001.fastq.gz127 | python /oak/stanford/groups/akundaje/marinovg/code/demultiplexFASTQDualIndex.py - SampleSheet-nonSHARE-seq.config 1 -prefix zz -suffix -L004-127
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py zzUndetermined_S0_L004_R1_001.fastq.gz128 zzUndetermined_S0_L004_R1_001.fastq.gz128 | python /oak/stanford/groups/akundaje/marinovg/code/demultiplexFASTQDualIndex.py - SampleSheet-nonSHARE-seq.config 1 -prefix zz -suffix -L004-128
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py zzUndetermined_S0_L004_R1_001.fastq.gz129 zzUndetermined_S0_L004_R1_001.fastq.gz129 | python /oak/stanford/groups/akundaje/marinovg/code/demultiplexFASTQDualIndex.py - SampleSheet-nonSHARE-seq.config 1 -prefix zz -suffix -L004-129
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py zzUndetermined_S0_L004_R1_001.fastq.gz13 zzUndetermined_S0_L004_R1_001.fastq.gz13 | python /oak/stanford/groups/akundaje/marinovg/code/demultiplexFASTQDualIndex.py - SampleSheet-nonSHARE-seq.config 1 -prefix zz -suffix -L004-13
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py zzUndetermined_S0_L004_R1_001.fastq.gz14 zzUndetermined_S0_L004_R1_001.fastq.gz14 | python /oak/stanford/groups/akundaje/marinovg/code/demultiplexFASTQDualIndex.py - SampleSheet-nonSHARE-seq.config 1 -prefix zz -suffix -L004-14
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py zzUndetermined_S0_L004_R1_001.fastq.gz15 zzUndetermined_S0_L004_R1_001.fastq.gz15 | python /oak/stanford/groups/akundaje/marinovg/code/demultiplexFASTQDualIndex.py - SampleSheet-nonSHARE-seq.config 1 -prefix zz -suffix -L004-15
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py zzUndetermined_S0_L004_R1_001.fastq.gz16 zzUndetermined_S0_L004_R1_001.fastq.gz16 | python /oak/stanford/groups/akundaje/marinovg/code/demultiplexFASTQDualIndex.py - SampleSheet-nonSHARE-seq.config 1 -prefix zz -suffix -L004-16
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py zzUndetermined_S0_L004_R1_001.fastq.gz17 zzUndetermined_S0_L004_R1_001.fastq.gz17 | python /oak/stanford/groups/akundaje/marinovg/code/demultiplexFASTQDualIndex.py - SampleSheet-nonSHARE-seq.config 1 -prefix zz -suffix -L004-17
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py zzUndetermined_S0_L004_R1_001.fastq.gz18 zzUndetermined_S0_L004_R1_001.fastq.gz18 | python /oak/stanford/groups/akundaje/marinovg/code/demultiplexFASTQDualIndex.py - SampleSheet-nonSHARE-seq.config 1 -prefix zz -suffix -L004-18
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py zzUndetermined_S0_L004_R1_001.fastq.gz19 zzUndetermined_S0_L004_R1_001.fastq.gz19 | python /oak/stanford/groups/akundaje/marinovg/code/demultiplexFASTQDualIndex.py - SampleSheet-nonSHARE-seq.config 1 -prefix zz -suffix -L004-19
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py zzUndetermined_S0_L004_R1_001.fastq.gz2 zzUndetermined_S0_L004_R1_001.fastq.gz2 | python /oak/stanford/groups/akundaje/marinovg/code/demultiplexFASTQDualIndex.py - SampleSheet-nonSHARE-seq.config 1 -prefix zz -suffix -L004-2
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py zzUndetermined_S0_L004_R1_001.fastq.gz20 zzUndetermined_S0_L004_R1_001.fastq.gz20 | python /oak/stanford/groups/akundaje/marinovg/code/demultiplexFASTQDualIndex.py - SampleSheet-nonSHARE-seq.config 1 -prefix zz -suffix -L004-20
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py zzUndetermined_S0_L004_R1_001.fastq.gz21 zzUndetermined_S0_L004_R1_001.fastq.gz21 | python /oak/stanford/groups/akundaje/marinovg/code/demultiplexFASTQDualIndex.py - SampleSheet-nonSHARE-seq.config 1 -prefix zz -suffix -L004-21
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py zzUndetermined_S0_L004_R1_001.fastq.gz22 zzUndetermined_S0_L004_R1_001.fastq.gz22 | python /oak/stanford/groups/akundaje/marinovg/code/demultiplexFASTQDualIndex.py - SampleSheet-nonSHARE-seq.config 1 -prefix zz -suffix -L004-22
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py zzUndetermined_S0_L004_R1_001.fastq.gz23 zzUndetermined_S0_L004_R1_001.fastq.gz23 | python /oak/stanford/groups/akundaje/marinovg/code/demultiplexFASTQDualIndex.py - SampleSheet-nonSHARE-seq.config 1 -prefix zz -suffix -L004-23
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py zzUndetermined_S0_L004_R1_001.fastq.gz24 zzUndetermined_S0_L004_R1_001.fastq.gz24 | python /oak/stanford/groups/akundaje/marinovg/code/demultiplexFASTQDualIndex.py - SampleSheet-nonSHARE-seq.config 1 -prefix zz -suffix -L004-24
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py zzUndetermined_S0_L004_R1_001.fastq.gz25 zzUndetermined_S0_L004_R1_001.fastq.gz25 | python /oak/stanford/groups/akundaje/marinovg/code/demultiplexFASTQDualIndex.py - SampleSheet-nonSHARE-seq.config 1 -prefix zz -suffix -L004-25
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py zzUndetermined_S0_L004_R1_001.fastq.gz26 zzUndetermined_S0_L004_R1_001.fastq.gz26 | python /oak/stanford/groups/akundaje/marinovg/code/demultiplexFASTQDualIndex.py - SampleSheet-nonSHARE-seq.config 1 -prefix zz -suffix -L004-26
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py zzUndetermined_S0_L004_R1_001.fastq.gz27 zzUndetermined_S0_L004_R1_001.fastq.gz27 | python /oak/stanford/groups/akundaje/marinovg/code/demultiplexFASTQDualIndex.py - SampleSheet-nonSHARE-seq.config 1 -prefix zz -suffix -L004-27
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py zzUndetermined_S0_L004_R1_001.fastq.gz28 zzUndetermined_S0_L004_R1_001.fastq.gz28 | python /oak/stanford/groups/akundaje/marinovg/code/demultiplexFASTQDualIndex.py - SampleSheet-nonSHARE-seq.config 1 -prefix zz -suffix -L004-28
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py zzUndetermined_S0_L004_R1_001.fastq.gz29 zzUndetermined_S0_L004_R1_001.fastq.gz29 | python /oak/stanford/groups/akundaje/marinovg/code/demultiplexFASTQDualIndex.py - SampleSheet-nonSHARE-seq.config 1 -prefix zz -suffix -L004-29
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py zzUndetermined_S0_L004_R1_001.fastq.gz3 zzUndetermined_S0_L004_R1_001.fastq.gz3 | python /oak/stanford/groups/akundaje/marinovg/code/demultiplexFASTQDualIndex.py - SampleSheet-nonSHARE-seq.config 1 -prefix zz -suffix -L004-3
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py zzUndetermined_S0_L004_R1_001.fastq.gz30 zzUndetermined_S0_L004_R1_001.fastq.gz30 | python /oak/stanford/groups/akundaje/marinovg/code/demultiplexFASTQDualIndex.py - SampleSheet-nonSHARE-seq.config 1 -prefix zz -suffix -L004-30
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py zzUndetermined_S0_L004_R1_001.fastq.gz31 zzUndetermined_S0_L004_R1_001.fastq.gz31 | python /oak/stanford/groups/akundaje/marinovg/code/demultiplexFASTQDualIndex.py - SampleSheet-nonSHARE-seq.config 1 -prefix zz -suffix -L004-31
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py zzUndetermined_S0_L004_R1_001.fastq.gz32 zzUndetermined_S0_L004_R1_001.fastq.gz32 | python /oak/stanford/groups/akundaje/marinovg/code/demultiplexFASTQDualIndex.py - SampleSheet-nonSHARE-seq.config 1 -prefix zz -suffix -L004-32
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py zzUndetermined_S0_L004_R1_001.fastq.gz33 zzUndetermined_S0_L004_R1_001.fastq.gz33 | python /oak/stanford/groups/akundaje/marinovg/code/demultiplexFASTQDualIndex.py - SampleSheet-nonSHARE-seq.config 1 -prefix zz -suffix -L004-33
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py zzUndetermined_S0_L004_R1_001.fastq.gz34 zzUndetermined_S0_L004_R1_001.fastq.gz34 | python /oak/stanford/groups/akundaje/marinovg/code/demultiplexFASTQDualIndex.py - SampleSheet-nonSHARE-seq.config 1 -prefix zz -suffix -L004-34
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py zzUndetermined_S0_L004_R1_001.fastq.gz35 zzUndetermined_S0_L004_R1_001.fastq.gz35 | python /oak/stanford/groups/akundaje/marinovg/code/demultiplexFASTQDualIndex.py - SampleSheet-nonSHARE-seq.config 1 -prefix zz -suffix -L004-35
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py zzUndetermined_S0_L004_R1_001.fastq.gz36 zzUndetermined_S0_L004_R1_001.fastq.gz36 | python /oak/stanford/groups/akundaje/marinovg/code/demultiplexFASTQDualIndex.py - SampleSheet-nonSHARE-seq.config 1 -prefix zz -suffix -L004-36
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py zzUndetermined_S0_L004_R1_001.fastq.gz37 zzUndetermined_S0_L004_R1_001.fastq.gz37 | python /oak/stanford/groups/akundaje/marinovg/code/demultiplexFASTQDualIndex.py - SampleSheet-nonSHARE-seq.config 1 -prefix zz -suffix -L004-37
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py zzUndetermined_S0_L004_R1_001.fastq.gz38 zzUndetermined_S0_L004_R1_001.fastq.gz38 | python /oak/stanford/groups/akundaje/marinovg/code/demultiplexFASTQDualIndex.py - SampleSheet-nonSHARE-seq.config 1 -prefix zz -suffix -L004-38
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py zzUndetermined_S0_L004_R1_001.fastq.gz39 zzUndetermined_S0_L004_R1_001.fastq.gz39 | python /oak/stanford/groups/akundaje/marinovg/code/demultiplexFASTQDualIndex.py - SampleSheet-nonSHARE-seq.config 1 -prefix zz -suffix -L004-39
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py zzUndetermined_S0_L004_R1_001.fastq.gz4 zzUndetermined_S0_L004_R1_001.fastq.gz4 | python /oak/stanford/groups/akundaje/marinovg/code/demultiplexFASTQDualIndex.py - SampleSheet-nonSHARE-seq.config 1 -prefix zz -suffix -L004-4
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py zzUndetermined_S0_L004_R1_001.fastq.gz40 zzUndetermined_S0_L004_R1_001.fastq.gz40 | python /oak/stanford/groups/akundaje/marinovg/code/demultiplexFASTQDualIndex.py - SampleSheet-nonSHARE-seq.config 1 -prefix zz -suffix -L004-40
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py zzUndetermined_S0_L004_R1_001.fastq.gz41 zzUndetermined_S0_L004_R1_001.fastq.gz41 | python /oak/stanford/groups/akundaje/marinovg/code/demultiplexFASTQDualIndex.py - SampleSheet-nonSHARE-seq.config 1 -prefix zz -suffix -L004-41
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py zzUndetermined_S0_L004_R1_001.fastq.gz42 zzUndetermined_S0_L004_R1_001.fastq.gz42 | python /oak/stanford/groups/akundaje/marinovg/code/demultiplexFASTQDualIndex.py - SampleSheet-nonSHARE-seq.config 1 -prefix zz -suffix -L004-42
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py zzUndetermined_S0_L004_R1_001.fastq.gz43 zzUndetermined_S0_L004_R1_001.fastq.gz43 | python /oak/stanford/groups/akundaje/marinovg/code/demultiplexFASTQDualIndex.py - SampleSheet-nonSHARE-seq.config 1 -prefix zz -suffix -L004-43
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py zzUndetermined_S0_L004_R1_001.fastq.gz44 zzUndetermined_S0_L004_R1_001.fastq.gz44 | python /oak/stanford/groups/akundaje/marinovg/code/demultiplexFASTQDualIndex.py - SampleSheet-nonSHARE-seq.config 1 -prefix zz -suffix -L004-44
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py zzUndetermined_S0_L004_R1_001.fastq.gz45 zzUndetermined_S0_L004_R1_001.fastq.gz45 | python /oak/stanford/groups/akundaje/marinovg/code/demultiplexFASTQDualIndex.py - SampleSheet-nonSHARE-seq.config 1 -prefix zz -suffix -L004-45
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py zzUndetermined_S0_L004_R1_001.fastq.gz46 zzUndetermined_S0_L004_R1_001.fastq.gz46 | python /oak/stanford/groups/akundaje/marinovg/code/demultiplexFASTQDualIndex.py - SampleSheet-nonSHARE-seq.config 1 -prefix zz -suffix -L004-46
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py zzUndetermined_S0_L004_R1_001.fastq.gz47 zzUndetermined_S0_L004_R1_001.fastq.gz47 | python /oak/stanford/groups/akundaje/marinovg/code/demultiplexFASTQDualIndex.py - SampleSheet-nonSHARE-seq.config 1 -prefix zz -suffix -L004-47
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py zzUndetermined_S0_L004_R1_001.fastq.gz48 zzUndetermined_S0_L004_R1_001.fastq.gz48 | python /oak/stanford/groups/akundaje/marinovg/code/demultiplexFASTQDualIndex.py - SampleSheet-nonSHARE-seq.config 1 -prefix zz -suffix -L004-48
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py zzUndetermined_S0_L004_R1_001.fastq.gz49 zzUndetermined_S0_L004_R1_001.fastq.gz49 | python /oak/stanford/groups/akundaje/marinovg/code/demultiplexFASTQDualIndex.py - SampleSheet-nonSHARE-seq.config 1 -prefix zz -suffix -L004-49
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py zzUndetermined_S0_L004_R1_001.fastq.gz5 zzUndetermined_S0_L004_R1_001.fastq.gz5 | python /oak/stanford/groups/akundaje/marinovg/code/demultiplexFASTQDualIndex.py - SampleSheet-nonSHARE-seq.config 1 -prefix zz -suffix -L004-5
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py zzUndetermined_S0_L004_R1_001.fastq.gz50 zzUndetermined_S0_L004_R1_001.fastq.gz50 | python /oak/stanford/groups/akundaje/marinovg/code/demultiplexFASTQDualIndex.py - SampleSheet-nonSHARE-seq.config 1 -prefix zz -suffix -L004-50
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py zzUndetermined_S0_L004_R1_001.fastq.gz51 zzUndetermined_S0_L004_R1_001.fastq.gz51 | python /oak/stanford/groups/akundaje/marinovg/code/demultiplexFASTQDualIndex.py - SampleSheet-nonSHARE-seq.config 1 -prefix zz -suffix -L004-51
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py zzUndetermined_S0_L004_R1_001.fastq.gz52 zzUndetermined_S0_L004_R1_001.fastq.gz52 | python /oak/stanford/groups/akundaje/marinovg/code/demultiplexFASTQDualIndex.py - SampleSheet-nonSHARE-seq.config 1 -prefix zz -suffix -L004-52
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py zzUndetermined_S0_L004_R1_001.fastq.gz53 zzUndetermined_S0_L004_R1_001.fastq.gz53 | python /oak/stanford/groups/akundaje/marinovg/code/demultiplexFASTQDualIndex.py - SampleSheet-nonSHARE-seq.config 1 -prefix zz -suffix -L004-53
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py zzUndetermined_S0_L004_R1_001.fastq.gz54 zzUndetermined_S0_L004_R1_001.fastq.gz54 | python /oak/stanford/groups/akundaje/marinovg/code/demultiplexFASTQDualIndex.py - SampleSheet-nonSHARE-seq.config 1 -prefix zz -suffix -L004-54
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py zzUndetermined_S0_L004_R1_001.fastq.gz55 zzUndetermined_S0_L004_R1_001.fastq.gz55 | python /oak/stanford/groups/akundaje/marinovg/code/demultiplexFASTQDualIndex.py - SampleSheet-nonSHARE-seq.config 1 -prefix zz -suffix -L004-55
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py zzUndetermined_S0_L004_R1_001.fastq.gz56 zzUndetermined_S0_L004_R1_001.fastq.gz56 | python /oak/stanford/groups/akundaje/marinovg/code/demultiplexFASTQDualIndex.py - SampleSheet-nonSHARE-seq.config 1 -prefix zz -suffix -L004-56
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py zzUndetermined_S0_L004_R1_001.fastq.gz57 zzUndetermined_S0_L004_R1_001.fastq.gz57 | python /oak/stanford/groups/akundaje/marinovg/code/demultiplexFASTQDualIndex.py - SampleSheet-nonSHARE-seq.config 1 -prefix zz -suffix -L004-57
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py zzUndetermined_S0_L004_R1_001.fastq.gz58 zzUndetermined_S0_L004_R1_001.fastq.gz58 | python /oak/stanford/groups/akundaje/marinovg/code/demultiplexFASTQDualIndex.py - SampleSheet-nonSHARE-seq.config 1 -prefix zz -suffix -L004-58
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py zzUndetermined_S0_L004_R1_001.fastq.gz59 zzUndetermined_S0_L004_R1_001.fastq.gz59 | python /oak/stanford/groups/akundaje/marinovg/code/demultiplexFASTQDualIndex.py - SampleSheet-nonSHARE-seq.config 1 -prefix zz -suffix -L004-59
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py zzUndetermined_S0_L004_R1_001.fastq.gz6 zzUndetermined_S0_L004_R1_001.fastq.gz6 | python /oak/stanford/groups/akundaje/marinovg/code/demultiplexFASTQDualIndex.py - SampleSheet-nonSHARE-seq.config 1 -prefix zz -suffix -L004-6
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py zzUndetermined_S0_L004_R1_001.fastq.gz60 zzUndetermined_S0_L004_R1_001.fastq.gz60 | python /oak/stanford/groups/akundaje/marinovg/code/demultiplexFASTQDualIndex.py - SampleSheet-nonSHARE-seq.config 1 -prefix zz -suffix -L004-60
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py zzUndetermined_S0_L004_R1_001.fastq.gz61 zzUndetermined_S0_L004_R1_001.fastq.gz61 | python /oak/stanford/groups/akundaje/marinovg/code/demultiplexFASTQDualIndex.py - SampleSheet-nonSHARE-seq.config 1 -prefix zz -suffix -L004-61
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py zzUndetermined_S0_L004_R1_001.fastq.gz62 zzUndetermined_S0_L004_R1_001.fastq.gz62 | python /oak/stanford/groups/akundaje/marinovg/code/demultiplexFASTQDualIndex.py - SampleSheet-nonSHARE-seq.config 1 -prefix zz -suffix -L004-62
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py zzUndetermined_S0_L004_R1_001.fastq.gz63 zzUndetermined_S0_L004_R1_001.fastq.gz63 | python /oak/stanford/groups/akundaje/marinovg/code/demultiplexFASTQDualIndex.py - SampleSheet-nonSHARE-seq.config 1 -prefix zz -suffix -L004-63
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py zzUndetermined_S0_L004_R1_001.fastq.gz64 zzUndetermined_S0_L004_R1_001.fastq.gz64 | python /oak/stanford/groups/akundaje/marinovg/code/demultiplexFASTQDualIndex.py - SampleSheet-nonSHARE-seq.config 1 -prefix zz -suffix -L004-64
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py zzUndetermined_S0_L004_R1_001.fastq.gz65 zzUndetermined_S0_L004_R1_001.fastq.gz65 | python /oak/stanford/groups/akundaje/marinovg/code/demultiplexFASTQDualIndex.py - SampleSheet-nonSHARE-seq.config 1 -prefix zz -suffix -L004-65
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py zzUndetermined_S0_L004_R1_001.fastq.gz66 zzUndetermined_S0_L004_R1_001.fastq.gz66 | python /oak/stanford/groups/akundaje/marinovg/code/demultiplexFASTQDualIndex.py - SampleSheet-nonSHARE-seq.config 1 -prefix zz -suffix -L004-66
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py zzUndetermined_S0_L004_R1_001.fastq.gz67 zzUndetermined_S0_L004_R1_001.fastq.gz67 | python /oak/stanford/groups/akundaje/marinovg/code/demultiplexFASTQDualIndex.py - SampleSheet-nonSHARE-seq.config 1 -prefix zz -suffix -L004-67
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py zzUndetermined_S0_L004_R1_001.fastq.gz68 zzUndetermined_S0_L004_R1_001.fastq.gz68 | python /oak/stanford/groups/akundaje/marinovg/code/demultiplexFASTQDualIndex.py - SampleSheet-nonSHARE-seq.config 1 -prefix zz -suffix -L004-68
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py zzUndetermined_S0_L004_R1_001.fastq.gz69 zzUndetermined_S0_L004_R1_001.fastq.gz69 | python /oak/stanford/groups/akundaje/marinovg/code/demultiplexFASTQDualIndex.py - SampleSheet-nonSHARE-seq.config 1 -prefix zz -suffix -L004-69
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py zzUndetermined_S0_L004_R1_001.fastq.gz7 zzUndetermined_S0_L004_R1_001.fastq.gz7 | python /oak/stanford/groups/akundaje/marinovg/code/demultiplexFASTQDualIndex.py - SampleSheet-nonSHARE-seq.config 1 -prefix zz -suffix -L004-7
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py zzUndetermined_S0_L004_R1_001.fastq.gz70 zzUndetermined_S0_L004_R1_001.fastq.gz70 | python /oak/stanford/groups/akundaje/marinovg/code/demultiplexFASTQDualIndex.py - SampleSheet-nonSHARE-seq.config 1 -prefix zz -suffix -L004-70
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py zzUndetermined_S0_L004_R1_001.fastq.gz71 zzUndetermined_S0_L004_R1_001.fastq.gz71 | python /oak/stanford/groups/akundaje/marinovg/code/demultiplexFASTQDualIndex.py - SampleSheet-nonSHARE-seq.config 1 -prefix zz -suffix -L004-71
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py zzUndetermined_S0_L004_R1_001.fastq.gz72 zzUndetermined_S0_L004_R1_001.fastq.gz72 | python /oak/stanford/groups/akundaje/marinovg/code/demultiplexFASTQDualIndex.py - SampleSheet-nonSHARE-seq.config 1 -prefix zz -suffix -L004-72
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py zzUndetermined_S0_L004_R1_001.fastq.gz73 zzUndetermined_S0_L004_R1_001.fastq.gz73 | python /oak/stanford/groups/akundaje/marinovg/code/demultiplexFASTQDualIndex.py - SampleSheet-nonSHARE-seq.config 1 -prefix zz -suffix -L004-73
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py zzUndetermined_S0_L004_R1_001.fastq.gz74 zzUndetermined_S0_L004_R1_001.fastq.gz74 | python /oak/stanford/groups/akundaje/marinovg/code/demultiplexFASTQDualIndex.py - SampleSheet-nonSHARE-seq.config 1 -prefix zz -suffix -L004-74
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py zzUndetermined_S0_L004_R1_001.fastq.gz75 zzUndetermined_S0_L004_R1_001.fastq.gz75 | python /oak/stanford/groups/akundaje/marinovg/code/demultiplexFASTQDualIndex.py - SampleSheet-nonSHARE-seq.config 1 -prefix zz -suffix -L004-75
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py zzUndetermined_S0_L004_R1_001.fastq.gz76 zzUndetermined_S0_L004_R1_001.fastq.gz76 | python /oak/stanford/groups/akundaje/marinovg/code/demultiplexFASTQDualIndex.py - SampleSheet-nonSHARE-seq.config 1 -prefix zz -suffix -L004-76
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py zzUndetermined_S0_L004_R1_001.fastq.gz77 zzUndetermined_S0_L004_R1_001.fastq.gz77 | python /oak/stanford/groups/akundaje/marinovg/code/demultiplexFASTQDualIndex.py - SampleSheet-nonSHARE-seq.config 1 -prefix zz -suffix -L004-77
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py zzUndetermined_S0_L004_R1_001.fastq.gz78 zzUndetermined_S0_L004_R1_001.fastq.gz78 | python /oak/stanford/groups/akundaje/marinovg/code/demultiplexFASTQDualIndex.py - SampleSheet-nonSHARE-seq.config 1 -prefix zz -suffix -L004-78
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py zzUndetermined_S0_L004_R1_001.fastq.gz79 zzUndetermined_S0_L004_R1_001.fastq.gz79 | python /oak/stanford/groups/akundaje/marinovg/code/demultiplexFASTQDualIndex.py - SampleSheet-nonSHARE-seq.config 1 -prefix zz -suffix -L004-79
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py zzUndetermined_S0_L004_R1_001.fastq.gz8 zzUndetermined_S0_L004_R1_001.fastq.gz8 | python /oak/stanford/groups/akundaje/marinovg/code/demultiplexFASTQDualIndex.py - SampleSheet-nonSHARE-seq.config 1 -prefix zz -suffix -L004-8
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py zzUndetermined_S0_L004_R1_001.fastq.gz80 zzUndetermined_S0_L004_R1_001.fastq.gz80 | python /oak/stanford/groups/akundaje/marinovg/code/demultiplexFASTQDualIndex.py - SampleSheet-nonSHARE-seq.config 1 -prefix zz -suffix -L004-80
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py zzUndetermined_S0_L004_R1_001.fastq.gz81 zzUndetermined_S0_L004_R1_001.fastq.gz81 | python /oak/stanford/groups/akundaje/marinovg/code/demultiplexFASTQDualIndex.py - SampleSheet-nonSHARE-seq.config 1 -prefix zz -suffix -L004-81
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py zzUndetermined_S0_L004_R1_001.fastq.gz82 zzUndetermined_S0_L004_R1_001.fastq.gz82 | python /oak/stanford/groups/akundaje/marinovg/code/demultiplexFASTQDualIndex.py - SampleSheet-nonSHARE-seq.config 1 -prefix zz -suffix -L004-82
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py zzUndetermined_S0_L004_R1_001.fastq.gz83 zzUndetermined_S0_L004_R1_001.fastq.gz83 | python /oak/stanford/groups/akundaje/marinovg/code/demultiplexFASTQDualIndex.py - SampleSheet-nonSHARE-seq.config 1 -prefix zz -suffix -L004-83
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py zzUndetermined_S0_L004_R1_001.fastq.gz84 zzUndetermined_S0_L004_R1_001.fastq.gz84 | python /oak/stanford/groups/akundaje/marinovg/code/demultiplexFASTQDualIndex.py - SampleSheet-nonSHARE-seq.config 1 -prefix zz -suffix -L004-84
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py zzUndetermined_S0_L004_R1_001.fastq.gz85 zzUndetermined_S0_L004_R1_001.fastq.gz85 | python /oak/stanford/groups/akundaje/marinovg/code/demultiplexFASTQDualIndex.py - SampleSheet-nonSHARE-seq.config 1 -prefix zz -suffix -L004-85
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py zzUndetermined_S0_L004_R1_001.fastq.gz86 zzUndetermined_S0_L004_R1_001.fastq.gz86 | python /oak/stanford/groups/akundaje/marinovg/code/demultiplexFASTQDualIndex.py - SampleSheet-nonSHARE-seq.config 1 -prefix zz -suffix -L004-86
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py zzUndetermined_S0_L004_R1_001.fastq.gz87 zzUndetermined_S0_L004_R1_001.fastq.gz87 | python /oak/stanford/groups/akundaje/marinovg/code/demultiplexFASTQDualIndex.py - SampleSheet-nonSHARE-seq.config 1 -prefix zz -suffix -L004-87
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py zzUndetermined_S0_L004_R1_001.fastq.gz88 zzUndetermined_S0_L004_R1_001.fastq.gz88 | python /oak/stanford/groups/akundaje/marinovg/code/demultiplexFASTQDualIndex.py - SampleSheet-nonSHARE-seq.config 1 -prefix zz -suffix -L004-88
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py zzUndetermined_S0_L004_R1_001.fastq.gz89 zzUndetermined_S0_L004_R1_001.fastq.gz89 | python /oak/stanford/groups/akundaje/marinovg/code/demultiplexFASTQDualIndex.py - SampleSheet-nonSHARE-seq.config 1 -prefix zz -suffix -L004-89
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py zzUndetermined_S0_L004_R1_001.fastq.gz9 zzUndetermined_S0_L004_R1_001.fastq.gz9 | python /oak/stanford/groups/akundaje/marinovg/code/demultiplexFASTQDualIndex.py - SampleSheet-nonSHARE-seq.config 1 -prefix zz -suffix -L004-9
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py zzUndetermined_S0_L004_R1_001.fastq.gz90 zzUndetermined_S0_L004_R1_001.fastq.gz90 | python /oak/stanford/groups/akundaje/marinovg/code/demultiplexFASTQDualIndex.py - SampleSheet-nonSHARE-seq.config 1 -prefix zz -suffix -L004-90
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py zzUndetermined_S0_L004_R1_001.fastq.gz91 zzUndetermined_S0_L004_R1_001.fastq.gz91 | python /oak/stanford/groups/akundaje/marinovg/code/demultiplexFASTQDualIndex.py - SampleSheet-nonSHARE-seq.config 1 -prefix zz -suffix -L004-91
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py zzUndetermined_S0_L004_R1_001.fastq.gz92 zzUndetermined_S0_L004_R1_001.fastq.gz92 | python /oak/stanford/groups/akundaje/marinovg/code/demultiplexFASTQDualIndex.py - SampleSheet-nonSHARE-seq.config 1 -prefix zz -suffix -L004-92
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py zzUndetermined_S0_L004_R1_001.fastq.gz93 zzUndetermined_S0_L004_R1_001.fastq.gz93 | python /oak/stanford/groups/akundaje/marinovg/code/demultiplexFASTQDualIndex.py - SampleSheet-nonSHARE-seq.config 1 -prefix zz -suffix -L004-93
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py zzUndetermined_S0_L004_R1_001.fastq.gz94 zzUndetermined_S0_L004_R1_001.fastq.gz94 | python /oak/stanford/groups/akundaje/marinovg/code/demultiplexFASTQDualIndex.py - SampleSheet-nonSHARE-seq.config 1 -prefix zz -suffix -L004-94
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py zzUndetermined_S0_L004_R1_001.fastq.gz95 zzUndetermined_S0_L004_R1_001.fastq.gz95 | python /oak/stanford/groups/akundaje/marinovg/code/demultiplexFASTQDualIndex.py - SampleSheet-nonSHARE-seq.config 1 -prefix zz -suffix -L004-95
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py zzUndetermined_S0_L004_R1_001.fastq.gz96 zzUndetermined_S0_L004_R1_001.fastq.gz96 | python /oak/stanford/groups/akundaje/marinovg/code/demultiplexFASTQDualIndex.py - SampleSheet-nonSHARE-seq.config 1 -prefix zz -suffix -L004-96
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py zzUndetermined_S0_L004_R1_001.fastq.gz97 zzUndetermined_S0_L004_R1_001.fastq.gz97 | python /oak/stanford/groups/akundaje/marinovg/code/demultiplexFASTQDualIndex.py - SampleSheet-nonSHARE-seq.config 1 -prefix zz -suffix -L004-97
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py zzUndetermined_S0_L004_R1_001.fastq.gz98 zzUndetermined_S0_L004_R1_001.fastq.gz98 | python /oak/stanford/groups/akundaje/marinovg/code/demultiplexFASTQDualIndex.py - SampleSheet-nonSHARE-seq.config 1 -prefix zz -suffix -L004-98
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py zzUndetermined_S0_L004_R1_001.fastq.gz99 zzUndetermined_S0_L004_R1_001.fastq.gz99 | python /oak/stanford/groups/akundaje/marinovg/code/demultiplexFASTQDualIndex.py - SampleSheet-nonSHARE-seq.config 1 -prefix zz -suffix -L004-99