python /oak/stanford/groups/akundaje/marinovg/code/transcriptome/gene_coverage_wig_gtf.py /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_microadriaticum_v1.0/Smic.genome.annotation.gtf smic_nn_R2-SRR3337493-TopHat-2.0.8/accepted_hits.unique.wig.gz 1000 coverage-smic_nn_R2-SRR3337493-TopHat-2.0.8.unique -normalize -singlemodelgenes
python /oak/stanford/groups/akundaje/marinovg/code/transcriptome/gene_coverage_wig_gtf.py /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_microadriaticum_v1.0/Smic.genome.annotation.gtf smic_nn_R3-SRR3337494-TopHat-2.0.8/accepted_hits.unique.wig.gz 1000 coverage-smic_nn_R3-SRR3337494-TopHat-2.0.8.unique -normalize -singlemodelgenes
python /oak/stanford/groups/akundaje/marinovg/code/transcriptome/gene_coverage_wig_gtf.py /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_microadriaticum_v1.0/Smic.genome.annotation.gtf smic_DS_R1-SRR3337495-TopHat-2.0.8/accepted_hits.unique.wig.gz 1000 coverage-smic_DS_R1-SRR3337495-TopHat-2.0.8.unique -normalize -singlemodelgenes
python /oak/stanford/groups/akundaje/marinovg/code/transcriptome/gene_coverage_wig_gtf.py /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_microadriaticum_v1.0/Smic.genome.annotation.gtf smic_DS_R2-SRR3337496-TopHat-2.0.8/accepted_hits.unique.wig.gz 1000 coverage-smic_DS_R2-SRR3337496-TopHat-2.0.8.unique -normalize -singlemodelgenes
python /oak/stanford/groups/akundaje/marinovg/code/transcriptome/gene_coverage_wig_gtf.py /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_microadriaticum_v1.0/Smic.genome.annotation.gtf smic_DS_R3-SRR3337497-TopHat-2.0.8/accepted_hits.unique.wig.gz 1000 coverage-smic_DS_R3-SRR3337497-TopHat-2.0.8.unique -normalize -singlemodelgenes
python /oak/stanford/groups/akundaje/marinovg/code/transcriptome/gene_coverage_wig_gtf.py /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_microadriaticum_v1.0/Smic.genome.annotation.gtf smic_nn_R1-SRR3337498-TopHat-2.0.8/accepted_hits.unique.wig.gz 1000 coverage-smic_nn_R1-SRR3337498-TopHat-2.0.8.unique -normalize -singlemodelgenes
python /oak/stanford/groups/akundaje/marinovg/code/transcriptome/gene_coverage_wig_gtf.py /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_microadriaticum_v1.0/Smic.genome.annotation.gtf smic_16C_R1-SRR3337500-TopHat-2.0.8/accepted_hits.unique.wig.gz 1000 coverage-smic_16C_R1-SRR3337500-TopHat-2.0.8.unique -normalize -singlemodelgenes
python /oak/stanford/groups/akundaje/marinovg/code/transcriptome/gene_coverage_wig_gtf.py /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_microadriaticum_v1.0/Smic.genome.annotation.gtf smic_16C_R2-SRR3337501-TopHat-2.0.8/accepted_hits.unique.wig.gz 1000 coverage-smic_16C_R2-SRR3337501-TopHat-2.0.8.unique -normalize -singlemodelgenes
python /oak/stanford/groups/akundaje/marinovg/code/transcriptome/gene_coverage_wig_gtf.py /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_microadriaticum_v1.0/Smic.genome.annotation.gtf smic_16C_R3-SRR3337502-TopHat-2.0.8/accepted_hits.unique.wig.gz 1000 coverage-smic_16C_R3-SRR3337502-TopHat-2.0.8.unique -normalize -singlemodelgenes
python /oak/stanford/groups/akundaje/marinovg/code/transcriptome/gene_coverage_wig_gtf.py /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_microadriaticum_v1.0/Smic.genome.annotation.gtf smic_36C_R1-SRR3337503-TopHat-2.0.8/accepted_hits.unique.wig.gz 1000 coverage-smic_36C_R1-SRR3337503-TopHat-2.0.8.unique -normalize -singlemodelgenes
python /oak/stanford/groups/akundaje/marinovg/code/transcriptome/gene_coverage_wig_gtf.py /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_microadriaticum_v1.0/Smic.genome.annotation.gtf smic_36C_R2-SRR3337504-TopHat-2.0.8/accepted_hits.unique.wig.gz 1000 coverage-smic_36C_R2-SRR3337504-TopHat-2.0.8.unique -normalize -singlemodelgenes
python /oak/stanford/groups/akundaje/marinovg/code/transcriptome/gene_coverage_wig_gtf.py /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_microadriaticum_v1.0/Smic.genome.annotation.gtf smic_36C_R3-SRR3337505-TopHat-2.0.8/accepted_hits.unique.wig.gz 1000 coverage-smic_36C_R3-SRR3337505-TopHat-2.0.8.unique -normalize -singlemodelgenes
python /oak/stanford/groups/akundaje/marinovg/code/transcriptome/gene_coverage_wig_gtf.py /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_microadriaticum_v1.0/Smic.genome.annotation.gtf smic_nn_R2-SRR3337493-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.unique.wig.gz 1000 coverage-smic_nn_R2-SRR3337493-STAR-2.5.3a.unique -normalize -singlemodelgenes
python /oak/stanford/groups/akundaje/marinovg/code/transcriptome/gene_coverage_wig_gtf.py /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_microadriaticum_v1.0/Smic.genome.annotation.gtf smic_nn_R3-SRR3337494-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.unique.wig.gz 1000 coverage-smic_nn_R3-SRR3337494-STAR-2.5.3a.unique -normalize -singlemodelgenes
python /oak/stanford/groups/akundaje/marinovg/code/transcriptome/gene_coverage_wig_gtf.py /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_microadriaticum_v1.0/Smic.genome.annotation.gtf smic_DS_R1-SRR3337495-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.unique.wig.gz 1000 coverage-smic_DS_R1-SRR3337495-STAR-2.5.3a.unique -normalize -singlemodelgenes
python /oak/stanford/groups/akundaje/marinovg/code/transcriptome/gene_coverage_wig_gtf.py /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_microadriaticum_v1.0/Smic.genome.annotation.gtf smic_DS_R2-SRR3337496-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.unique.wig.gz 1000 coverage-smic_DS_R2-SRR3337496-STAR-2.5.3a.unique -normalize -singlemodelgenes
python /oak/stanford/groups/akundaje/marinovg/code/transcriptome/gene_coverage_wig_gtf.py /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_microadriaticum_v1.0/Smic.genome.annotation.gtf smic_DS_R3-SRR3337497-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.unique.wig.gz 1000 coverage-smic_DS_R3-SRR3337497-STAR-2.5.3a.unique -normalize -singlemodelgenes
python /oak/stanford/groups/akundaje/marinovg/code/transcriptome/gene_coverage_wig_gtf.py /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_microadriaticum_v1.0/Smic.genome.annotation.gtf smic_nn_R1-SRR3337498-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.unique.wig.gz 1000 coverage-smic_nn_R1-SRR3337498-STAR-2.5.3a.unique -normalize -singlemodelgenes
python /oak/stanford/groups/akundaje/marinovg/code/transcriptome/gene_coverage_wig_gtf.py /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_microadriaticum_v1.0/Smic.genome.annotation.gtf smic_16C_R1-SRR3337500-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.unique.wig.gz 1000 coverage-smic_16C_R1-SRR3337500-STAR-2.5.3a.unique -normalize -singlemodelgenes
python /oak/stanford/groups/akundaje/marinovg/code/transcriptome/gene_coverage_wig_gtf.py /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_microadriaticum_v1.0/Smic.genome.annotation.gtf smic_16C_R2-SRR3337501-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.unique.wig.gz 1000 coverage-smic_16C_R2-SRR3337501-STAR-2.5.3a.unique -normalize -singlemodelgenes
python /oak/stanford/groups/akundaje/marinovg/code/transcriptome/gene_coverage_wig_gtf.py /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_microadriaticum_v1.0/Smic.genome.annotation.gtf smic_16C_R3-SRR3337502-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.unique.wig.gz 1000 coverage-smic_16C_R3-SRR3337502-STAR-2.5.3a.unique -normalize -singlemodelgenes
python /oak/stanford/groups/akundaje/marinovg/code/transcriptome/gene_coverage_wig_gtf.py /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_microadriaticum_v1.0/Smic.genome.annotation.gtf smic_36C_R1-SRR3337503-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.unique.wig.gz 1000 coverage-smic_36C_R1-SRR3337503-STAR-2.5.3a.unique -normalize -singlemodelgenes
python /oak/stanford/groups/akundaje/marinovg/code/transcriptome/gene_coverage_wig_gtf.py /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_microadriaticum_v1.0/Smic.genome.annotation.gtf smic_36C_R2-SRR3337504-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.unique.wig.gz 1000 coverage-smic_36C_R2-SRR3337504-STAR-2.5.3a.unique -normalize -singlemodelgenes
python /oak/stanford/groups/akundaje/marinovg/code/transcriptome/gene_coverage_wig_gtf.py /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_microadriaticum_v1.0/Smic.genome.annotation.gtf smic_36C_R3-SRR3337505-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.unique.wig.gz 1000 coverage-smic_36C_R3-SRR3337505-STAR-2.5.3a.unique -normalize -singlemodelgenes