python /oak/stanford/groups/akundaje/marinovg/code/transcriptome/SAM_reads_in_genes4_BAM.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.bam /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_microadriaticum_v1.0/Smic.genome.scaffold.final.chrom.sizes sam_reads_in_genes_v4-smic_nn_R2-SRR3337493-TopHat-2.0.8 -nomulti
python /oak/stanford/groups/akundaje/marinovg/code/transcriptome/SAM_reads_in_genes4_BAM.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.bam /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_microadriaticum_v1.0/Smic.genome.scaffold.final.chrom.sizes sam_reads_in_genes-smic_36C_R2-SRR3337504-STAR-2.5.3a -nomulti
python /oak/stanford/groups/akundaje/marinovg/code/transcriptome/SAM_reads_in_genes4_BAM.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.bam /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_microadriaticum_v1.0/Smic.genome.scaffold.final.chrom.sizes sam_reads_in_genes-smic_16C_R1-SRR3337500-STAR-2.5.3a -nomulti
python /oak/stanford/groups/akundaje/marinovg/code/transcriptome/SAM_reads_in_genes4_BAM.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.bam /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_microadriaticum_v1.0/Smic.genome.scaffold.final.chrom.sizes sam_reads_in_genes-smic_DS_R2-SRR3337496-STAR-2.5.3a -nomulti