nucleoatac occ --bed symbB.v1.0.genome.chunks.bed0 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-0  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed1 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-1  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed10 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-10  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed100 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-100  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed101 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-101  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed102 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-102  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed103 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-103  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed104 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-104  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed105 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-105  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed106 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-106  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed107 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-107  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed108 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-108  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed109 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-109  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed11 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-11  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed110 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-110  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed111 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-111  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed112 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-112  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed113 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-113  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed114 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-114  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed115 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-115  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed116 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-116  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed117 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-117  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed118 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-118  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed119 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-119  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed12 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-12  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed120 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-120  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed121 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-121  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed122 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-122  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed123 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-123  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed124 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-124  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed125 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-125  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed126 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-126  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed127 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-127  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed128 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-128  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed129 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-129  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed13 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-13  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed130 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-130  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed131 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-131  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed132 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-132  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed133 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-133  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed134 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-134  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed135 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-135  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed136 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-136  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed137 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-137  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed138 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-138  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed139 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-139  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed14 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-14  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed140 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-140  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed141 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-141  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed142 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-142  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed143 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-143  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed144 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-144  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed145 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-145  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed146 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-146  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed147 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-147  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed148 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-148  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed149 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-149  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed15 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-15  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed150 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-150  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed151 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-151  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed152 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-152  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed153 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-153  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed154 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-154  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed155 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-155  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed156 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-156  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed157 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-157  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed158 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-158  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed159 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-159  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed16 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-16  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed160 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-160  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed161 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-161  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed162 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-162  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed163 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-163  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed164 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-164  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed165 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-165  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed166 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-166  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed167 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-167  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed168 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-168  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed169 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-169  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed17 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-17  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed170 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-170  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed171 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-171  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed172 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-172  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed173 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-173  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed174 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-174  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed175 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-175  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed176 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-176  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed177 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-177  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed178 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-178  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed179 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-179  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed18 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-18  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed180 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-180  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed181 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-181  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed182 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-182  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed183 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-183  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed184 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-184  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed185 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-185  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed186 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-186  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed187 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-187  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed188 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-188  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed189 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-189  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed19 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-19  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed190 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-190  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed191 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-191  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed192 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-192  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed193 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-193  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed194 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-194  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed195 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-195  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed196 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-196  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed197 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-197  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed198 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-198  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed199 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-199  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed2 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-2  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed20 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-20  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed200 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-200  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed201 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-201  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed202 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-202  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed203 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-203  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed204 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-204  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed205 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-205  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed206 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-206  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed207 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-207  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed208 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-208  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed209 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-209  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed21 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-21  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed210 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-210  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed211 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-211  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed212 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-212  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed213 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-213  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed214 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-214  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed215 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-215  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed216 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-216  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed217 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-217  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed218 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-218  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed219 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-219  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed22 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-22  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed220 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-220  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed221 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-221  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed222 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-222  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed223 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-223  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed224 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-224  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed225 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-225  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed226 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-226  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed227 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-227  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed228 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-228  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed229 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-229  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed23 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-23  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed230 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-230  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed231 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-231  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed232 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-232  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed233 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-233  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed234 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-234  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed235 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-235  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed236 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-236  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed237 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-237  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed238 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-238  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed239 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-239  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed24 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-24  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed240 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-240  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed241 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-241  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed242 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-242  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed243 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-243  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed244 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-244  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed245 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-245  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed246 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-246  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed247 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-247  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed248 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-248  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed249 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-249  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed25 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-25  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed250 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-250  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed251 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-251  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed252 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-252  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed253 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-253  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed254 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-254  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed255 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-255  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed256 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-256  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed257 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-257  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed258 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-258  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed259 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-259  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed26 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-26  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed260 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-260  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed261 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-261  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed262 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-262  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed263 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-263  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed264 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-264  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed265 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-265  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed266 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-266  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed267 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-267  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed268 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-268  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed269 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-269  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed27 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-27  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed270 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-270  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed271 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-271  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed272 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-272  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed273 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-273  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed274 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-274  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed275 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-275  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed276 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-276  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed277 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-277  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed278 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-278  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed279 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-279  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed28 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-28  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed280 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-280  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed281 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-281  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed282 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-282  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed283 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-283  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed284 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-284  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed285 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-285  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed286 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-286  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed287 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-287  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed288 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-288  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed289 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-289  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed29 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-29  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed290 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-290  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed291 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-291  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed292 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-292  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed293 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-293  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed294 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-294  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed295 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-295  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed296 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-296  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed297 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-297  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed298 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-298  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed299 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-299  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed3 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-3  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed30 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-30  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed300 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-300  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed301 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-301  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed302 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-302  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed303 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-303  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed304 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-304  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed305 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-305  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed306 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-306  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed307 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-307  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed308 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-308  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed309 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-309  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed31 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-31  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed310 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-310  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed311 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-311  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed312 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-312  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed313 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-313  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed314 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-314  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed315 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-315  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed316 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-316  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed317 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-317  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed318 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-318  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed319 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-319  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed32 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-32  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed320 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-320  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed321 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-321  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed322 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-322  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed323 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-323  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed324 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-324  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed325 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-325  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed326 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-326  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed327 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-327  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed328 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-328  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed329 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-329  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed33 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-33  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed330 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-330  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed331 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-331  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed332 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-332  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed333 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-333  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed334 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-334  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed335 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-335  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed336 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-336  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed337 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-337  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed338 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-338  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed339 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-339  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed34 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-34  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed340 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-340  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed341 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-341  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed342 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-342  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed343 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-343  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed344 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-344  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed345 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-345  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed346 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-346  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed347 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-347  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed348 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-348  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed349 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-349  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed35 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-35  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed350 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-350  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed351 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-351  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed352 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-352  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed353 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-353  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed354 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-354  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed355 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-355  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed356 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-356  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed357 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-357  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed358 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-358  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed359 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-359  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed36 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-36  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed360 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-360  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed361 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-361  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed362 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-362  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed363 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-363  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed364 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-364  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed365 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-365  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed366 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-366  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed367 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-367  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed368 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-368  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed369 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-369  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed37 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-37  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed370 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-370  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed371 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-371  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed372 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-372  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed373 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-373  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed374 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-374  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed375 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-375  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed376 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-376  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed377 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-377  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed378 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-378  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed379 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-379  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed38 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-38  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed380 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-380  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed381 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-381  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed382 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-382  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed383 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-383  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed384 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-384  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed385 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-385  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed386 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-386  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed387 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-387  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed388 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-388  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed389 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-389  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed39 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-39  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed390 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-390  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed391 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-391  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed392 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-392  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed393 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-393  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed394 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-394  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed395 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-395  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed396 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-396  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed397 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-397  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed398 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-398  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed399 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-399  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed4 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-4  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed40 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-40  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed400 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-400  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed401 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-401  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed402 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-402  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed403 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-403  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed404 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-404  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed405 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-405  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed406 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-406  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed407 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-407  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed408 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-408  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed409 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-409  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed41 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-41  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed410 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-410  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed411 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-411  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed412 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-412  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed413 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-413  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed414 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-414  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed415 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-415  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed416 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-416  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed417 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-417  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed418 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-418  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed419 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-419  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed42 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-42  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed420 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-420  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed421 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-421  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed422 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-422  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed423 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-423  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed424 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-424  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed425 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-425  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed426 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-426  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed427 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-427  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed428 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-428  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed429 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-429  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed43 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-43  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed430 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-430  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed431 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-431  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed432 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-432  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed433 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-433  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed434 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-434  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed435 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-435  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed436 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-436  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed437 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-437  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed438 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-438  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed439 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-439  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed44 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-44  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed440 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-440  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed441 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-441  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed442 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-442  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed443 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-443  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed444 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-444  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed445 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-445  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed446 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-446  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed447 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-447  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed448 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-448  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed449 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-449  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed45 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-45  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed450 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-450  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed451 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-451  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed452 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-452  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed453 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-453  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed454 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-454  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed455 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-455  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed456 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-456  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed457 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-457  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed458 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-458  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed459 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-459  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed46 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-46  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed460 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-460  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed461 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-461  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed462 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-462  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed463 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-463  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed464 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-464  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed465 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-465  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed466 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-466  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed467 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-467  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed468 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-468  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed469 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-469  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed47 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-47  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed470 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-470  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed471 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-471  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed472 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-472  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed473 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-473  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed474 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-474  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed475 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-475  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed476 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-476  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed477 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-477  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed478 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-478  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed479 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-479  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed48 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-48  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed480 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-480  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed481 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-481  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed482 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-482  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed483 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-483  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed484 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-484  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed485 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-485  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed486 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-486  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed487 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-487  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed488 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-488  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed489 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-489  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed49 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-49  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed490 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-490  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed491 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-491  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed492 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-492  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed493 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-493  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed494 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-494  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed495 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-495  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed496 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-496  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed497 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-497  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed498 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-498  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed499 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-499  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed5 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-5  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed50 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-50  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed500 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-500  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed501 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-501  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed502 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-502  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed503 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-503  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed504 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-504  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed505 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-505  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed506 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-506  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed507 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-507  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed508 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-508  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed509 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-509  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed51 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-51  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed510 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-510  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed511 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-511  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed512 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-512  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed513 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-513  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed514 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-514  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed515 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-515  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed516 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-516  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed517 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-517  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed518 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-518  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed519 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-519  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed52 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-52  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed520 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-520  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed521 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-521  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed522 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-522  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed523 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-523  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed524 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-524  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed525 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-525  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed526 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-526  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed527 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-527  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed528 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-528  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed529 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-529  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed53 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-53  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed530 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-530  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed531 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-531  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed532 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-532  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed533 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-533  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed534 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-534  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed535 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-535  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed536 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-536  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed537 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-537  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed538 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-538  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed539 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-539  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed54 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-54  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed540 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-540  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed541 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-541  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed542 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-542  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed543 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-543  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed544 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-544  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed545 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-545  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed546 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-546  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed547 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-547  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed548 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-548  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed549 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-549  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed55 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-55  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed550 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-550  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed551 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-551  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed552 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-552  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed553 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-553  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed554 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-554  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed555 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-555  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed556 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-556  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed557 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-557  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed558 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-558  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed559 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-559  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed56 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-56  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed560 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-560  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed561 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-561  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed562 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-562  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed563 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-563  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed564 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-564  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed565 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-565  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed566 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-566  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed567 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-567  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed568 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-568  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed569 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-569  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed57 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-57  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed570 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-570  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed571 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-571  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed572 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-572  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed573 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-573  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed574 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-574  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed575 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-575  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed576 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-576  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed577 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-577  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed578 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-578  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed579 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-579  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed58 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-58  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed580 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-580  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed581 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-581  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed582 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-582  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed583 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-583  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed584 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-584  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed585 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-585  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed586 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-586  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed587 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-587  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed588 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-588  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed589 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-589  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed59 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-59  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed590 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-590  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed591 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-591  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed592 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-592  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed593 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-593  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed594 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-594  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed595 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-595  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed596 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-596  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed597 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-597  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed598 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-598  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed599 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-599  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed6 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-6  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed60 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-60  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed600 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-600  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed601 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-601  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed602 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-602  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed603 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-603  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed604 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-604  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed605 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-605  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed606 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-606  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed607 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-607  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed608 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-608  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed609 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-609  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed61 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-61  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed610 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-610  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed611 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-611  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed612 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-612  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed613 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-613  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed614 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-614  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed615 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-615  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed616 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-616  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed617 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-617  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed618 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-618  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed619 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-619  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed62 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-62  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed620 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-620  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed621 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-621  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed622 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-622  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed623 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-623  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed624 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-624  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed625 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-625  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed626 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-626  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed627 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-627  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed628 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-628  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed629 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-629  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed63 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-63  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed630 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-630  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed631 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-631  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed632 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-632  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed633 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-633  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed634 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-634  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed635 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-635  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed636 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-636  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed637 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-637  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed638 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-638  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed639 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-639  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed64 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-64  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed640 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-640  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed641 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-641  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed642 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-642  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed643 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-643  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed644 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-644  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed645 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-645  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed646 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-646  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed647 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-647  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed648 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-648  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed649 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-649  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed65 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-65  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed650 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-650  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed651 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-651  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed652 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-652  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed653 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-653  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed654 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-654  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed655 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-655  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed656 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-656  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed657 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-657  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed658 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-658  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed659 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-659  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed66 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-66  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed660 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-660  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed661 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-661  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed662 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-662  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed663 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-663  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed664 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-664  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed665 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-665  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed666 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-666  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed667 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-667  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed668 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-668  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed669 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-669  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed67 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-67  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed670 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-670  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed671 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-671  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed672 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-672  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed673 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-673  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed674 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-674  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed675 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-675  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed676 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-676  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed677 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-677  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed678 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-678  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed679 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-679  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed68 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-68  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed680 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-680  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed681 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-681  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed682 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-682  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed683 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-683  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed684 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-684  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed685 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-685  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed686 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-686  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed687 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-687  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed688 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-688  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed689 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-689  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed69 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-69  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed690 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-690  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed691 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-691  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed692 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-692  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed693 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-693  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed694 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-694  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed695 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-695  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed696 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-696  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed697 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-697  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed698 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-698  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed699 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-699  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed7 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-7  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed70 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-70  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed700 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-700  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed701 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-701  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed702 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-702  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed703 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-703  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed704 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-704  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed705 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-705  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed706 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-706  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed707 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-707  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed708 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-708  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed709 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-709  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed71 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-71  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed710 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-710  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed711 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-711  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed712 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-712  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed713 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-713  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed714 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-714  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed715 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-715  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed716 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-716  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed717 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-717  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed718 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-718  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed719 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-719  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed72 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-72  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed720 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-720  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed721 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-721  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed722 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-722  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed723 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-723  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed724 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-724  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed725 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-725  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed726 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-726  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed727 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-727  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed728 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-728  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed729 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-729  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed73 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-73  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed730 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-730  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed731 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-731  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed732 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-732  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed733 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-733  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed734 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-734  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed735 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-735  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed736 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-736  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed737 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-737  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed738 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-738  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed739 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-739  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed74 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-74  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed740 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-740  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed741 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-741  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed742 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-742  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed743 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-743  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed744 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-744  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed745 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-745  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed746 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-746  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed747 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-747  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed748 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-748  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed749 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-749  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed75 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-75  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed750 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-750  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed751 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-751  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed752 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-752  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed753 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-753  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed754 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-754  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed755 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-755  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed756 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-756  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed757 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-757  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed758 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-758  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed759 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-759  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed76 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-76  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed760 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-760  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed761 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-761  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed762 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-762  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed763 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-763  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed764 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-764  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed765 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-765  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed766 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-766  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed767 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-767  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed768 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-768  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed769 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-769  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed77 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-77  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed770 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-770  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed771 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-771  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed772 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-772  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed773 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-773  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed774 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-774  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed775 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-775  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed776 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-776  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed777 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-777  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed778 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-778  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed779 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-779  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed78 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-78  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed780 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-780  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed781 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-781  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed782 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-782  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed783 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-783  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed784 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-784  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed785 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-785  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed786 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-786  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed787 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-787  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed788 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-788  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed789 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-789  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed79 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-79  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed790 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-790  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed791 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-791  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed792 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-792  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed793 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-793  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed794 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-794  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed795 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-795  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed796 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-796  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed797 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-797  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed798 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-798  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed799 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-799  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed8 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-8  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed80 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-80  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed800 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-800  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed801 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-801  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed802 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-802  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed803 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-803  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed804 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-804  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed805 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-805  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed806 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-806  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed807 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-807  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed808 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-808  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed809 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-809  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed81 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-81  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed810 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-810  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed811 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-811  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed812 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-812  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed813 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-813  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed814 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-814  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed815 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-815  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed816 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-816  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed817 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-817  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed818 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-818  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed819 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-819  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed82 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-82  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed820 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-820  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed821 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-821  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed822 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-822  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed823 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-823  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed824 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-824  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed825 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-825  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed826 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-826  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed827 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-827  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed828 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-828  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed829 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-829  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed83 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-83  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed830 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-830  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed831 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-831  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed832 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-832  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed833 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-833  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed834 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-834  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed835 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-835  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed836 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-836  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed837 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-837  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed838 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-838  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed839 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-839  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed84 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-84  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed840 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-840  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed841 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-841  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed842 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-842  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed843 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-843  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed844 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-844  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed845 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-845  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed846 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-846  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed847 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-847  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed848 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-848  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed849 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-849  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed85 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-85  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed850 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-850  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed851 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-851  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed852 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-852  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed853 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-853  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed854 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-854  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed855 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-855  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed856 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-856  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed857 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-857  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed858 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-858  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed859 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-859  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed86 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-86  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed860 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-860  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed861 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-861  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed862 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-862  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed863 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-863  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed864 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-864  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed865 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-865  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed866 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-866  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed867 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-867  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed868 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-868  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed869 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-869  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed87 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-87  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed870 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-870  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed871 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-871  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed872 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-872  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed873 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-873  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed874 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-874  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed875 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-875  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed876 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-876  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed877 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-877  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed878 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-878  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed879 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-879  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed88 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-88  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed880 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-880  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed881 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-881  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed882 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-882  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed883 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-883  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed884 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-884  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed885 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-885  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed886 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-886  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed887 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-887  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed888 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-888  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed889 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-889  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed89 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-89  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed890 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-890  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed891 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-891  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed892 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-892  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed893 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-893  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed894 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-894  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed895 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-895  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed896 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-896  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed897 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-897  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed898 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-898  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed899 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-899  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed9 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-9  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed90 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-90  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed900 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-900  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed901 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-901  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed902 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-902  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed903 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-903  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed904 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-904  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed905 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-905  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed906 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-906  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed907 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-907  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed908 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-908  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed909 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-909  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed91 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-91  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed910 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-910  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed911 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-911  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed912 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-912  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed913 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-913  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed914 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-914  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed915 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-915  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed916 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-916  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed917 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-917  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed918 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-918  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed919 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-919  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed92 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-92  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed920 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-920  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed921 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-921  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed922 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-922  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed923 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-923  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed924 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-924  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed925 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-925  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed926 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-926  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed927 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-927  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed928 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-928  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed929 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-929  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed93 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-93  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed930 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-930  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed931 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-931  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed932 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-932  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed933 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-933  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed934 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-934  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed935 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-935  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed936 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-936  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed937 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-937  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed938 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-938  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed939 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-939  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed94 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-94  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed940 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-940  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed941 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-941  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed942 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-942  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed943 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-943  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed944 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-944  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed945 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-945  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed946 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-946  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed947 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-947  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed948 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-948  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed949 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-949  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed95 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-95  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed950 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-950  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed951 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-951  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed952 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-952  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed953 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-953  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed954 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-954  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed955 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-955  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed956 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-956  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed957 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-957  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed958 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-958  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed959 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-959  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed96 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-96  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed960 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-960  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed961 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-961  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed962 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-962  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed963 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-963  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed964 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-964  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed965 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-965  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed966 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-966  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed967 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-967  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed968 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-968  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed969 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-969  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed97 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-97  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed970 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-970  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed971 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-971  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed972 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-972  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed973 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-973  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed974 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-974  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed975 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-975  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed976 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-976  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed977 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-977  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed978 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-978  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed979 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-979  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed98 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-98  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed980 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-980  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed981 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-981  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed982 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-982  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed983 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-983  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed984 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-984  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed985 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-985  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed986 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-986  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed987 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-987  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed988 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-988  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed989 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-989  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed99 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-99  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed990 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-990  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed991 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-991  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed992 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-992  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed993 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-993  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed994 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-994  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed995 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-995  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed996 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-996  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed997 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-997  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed998 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-998  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa
nucleoatac occ --bed symbB.v1.0.genome.chunks.bed999 --bam L08_Symbiodinium_minutum_SSb01_omniATAC.2x36mers.symbB.v1.0.a.shuffled.bam --out nucleoatac-occ-999  --fasta /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa