python /oak/stanford/groups/akundaje/marinovg/code/transcriptome/junctionsfromBAM.py SRR870465-TopHat-2.0.8/accepted_hits.bam /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/symbB.v1.0.genome.chrom.sizes SRR870465-TopHat-2.0.8/junctions.bed bed SRR870465-TopHat-2.0.8/accepted_hits.juncs
python /oak/stanford/groups/akundaje/marinovg/code/transcriptome/junctionsfromBAM.py SRR870466-TopHat-2.0.8/accepted_hits.bam /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/symbB.v1.0.genome.chrom.sizes SRR870466-TopHat-2.0.8/junctions.bed bed SRR870466-TopHat-2.0.8/accepted_hits.juncs
python /oak/stanford/groups/akundaje/marinovg/code/transcriptome/junctionsfromBAM.py SRR870467-TopHat-2.0.8/accepted_hits.bam /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/symbB.v1.0.genome.chrom.sizes SRR870467-TopHat-2.0.8/junctions.bed bed SRR870467-TopHat-2.0.8/accepted_hits.juncs
python /oak/stanford/groups/akundaje/marinovg/code/transcriptome/junctionsfromBAM.py SRR870507-TopHat-2.0.8/accepted_hits.bam /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/symbB.v1.0.genome.chrom.sizes SRR870507-TopHat-2.0.8/junctions.bed bed SRR870507-TopHat-2.0.8/accepted_hits.juncs
python /oak/stanford/groups/akundaje/marinovg/code/transcriptome/junctionsfromBAM.py SRR870508-TopHat-2.0.8/accepted_hits.bam /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/symbB.v1.0.genome.chrom.sizes SRR870508-TopHat-2.0.8/junctions.bed bed SRR870508-TopHat-2.0.8/accepted_hits.juncs
python /oak/stanford/groups/akundaje/marinovg/code/transcriptome/junctionsfromBAM.py SRR870509-TopHat-2.0.8/accepted_hits.bam /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/symbB.v1.0.genome.chrom.sizes SRR870509-TopHat-2.0.8/junctions.bed bed SRR870509-TopHat-2.0.8/accepted_hits.juncs
python /oak/stanford/groups/akundaje/marinovg/code/transcriptome/junctionsfromBAM.py SRR870516-TopHat-2.0.8/accepted_hits.bam /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/symbB.v1.0.genome.chrom.sizes SRR870516-TopHat-2.0.8/junctions.bed bed SRR870516-TopHat-2.0.8/accepted_hits.juncs
python /oak/stanford/groups/akundaje/marinovg/code/transcriptome/junctionsfromBAM.py SRR870522-TopHat-2.0.8/accepted_hits.bam /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/symbB.v1.0.genome.chrom.sizes SRR870522-TopHat-2.0.8/junctions.bed bed SRR870522-TopHat-2.0.8/accepted_hits.juncs
python /oak/stanford/groups/akundaje/marinovg/code/transcriptome/junctionsfromBAM.py SRR870524-TopHat-2.0.8/accepted_hits.bam /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/symbB.v1.0.genome.chrom.sizes SRR870524-TopHat-2.0.8/junctions.bed bed SRR870524-TopHat-2.0.8/accepted_hits.juncs
python /oak/stanford/groups/akundaje/marinovg/code/transcriptome/junctionsfromBAM.py SRR870525-TopHat-2.0.8/accepted_hits.bam /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/symbB.v1.0.genome.chrom.sizes SRR870525-TopHat-2.0.8/junctions.bed bed SRR870525-TopHat-2.0.8/accepted_hits.juncs