python /oak/stanford/groups/akundaje/marinovg/code/transcriptome/SAM_reads_in_genes3_BAM.py /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Echinodermata/Strongylocentrotus_purpuratus-Spur_5.0/Strongylocentrotus_purpuratus-Spur_5.0.fixed.gtf Total_RNA_0hpf-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Echinodermata/Strongylocentrotus_purpuratus-Spur_5.0/Strongylocentrotus_purpuratus-Spur_5.0.chrom.sizes  sam_reads_in_genes-Total_RNA_0hpf -nomulti
python /oak/stanford/groups/akundaje/marinovg/code/transcriptome/SAM_reads_in_genes3_BAM.py /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Echinodermata/Strongylocentrotus_purpuratus-Spur_5.0/Strongylocentrotus_purpuratus-Spur_5.0.fixed.gtf Total_RNA_12hpf-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Echinodermata/Strongylocentrotus_purpuratus-Spur_5.0/Strongylocentrotus_purpuratus-Spur_5.0.chrom.sizes  sam_reads_in_genes-Total_RNA_12hpf -nomulti
python /oak/stanford/groups/akundaje/marinovg/code/transcriptome/SAM_reads_in_genes3_BAM.py /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Echinodermata/Strongylocentrotus_purpuratus-Spur_5.0/Strongylocentrotus_purpuratus-Spur_5.0.fixed.gtf Total_RNA_18hpf-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Echinodermata/Strongylocentrotus_purpuratus-Spur_5.0/Strongylocentrotus_purpuratus-Spur_5.0.chrom.sizes  sam_reads_in_genes-Total_RNA_18hpf -nomulti
python /oak/stanford/groups/akundaje/marinovg/code/transcriptome/SAM_reads_in_genes3_BAM.py /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Echinodermata/Strongylocentrotus_purpuratus-Spur_5.0/Strongylocentrotus_purpuratus-Spur_5.0.fixed.gtf Total_RNA_24hpf-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Echinodermata/Strongylocentrotus_purpuratus-Spur_5.0/Strongylocentrotus_purpuratus-Spur_5.0.chrom.sizes  sam_reads_in_genes-Total_RNA_24hpf -nomulti
python /oak/stanford/groups/akundaje/marinovg/code/transcriptome/SAM_reads_in_genes3_BAM.py /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Echinodermata/Strongylocentrotus_purpuratus-Spur_5.0/Strongylocentrotus_purpuratus-Spur_5.0.fixed.gtf Total_RNA_30hpf-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Echinodermata/Strongylocentrotus_purpuratus-Spur_5.0/Strongylocentrotus_purpuratus-Spur_5.0.chrom.sizes  sam_reads_in_genes-Total_RNA_30hpf -nomulti
python /oak/stanford/groups/akundaje/marinovg/code/transcriptome/SAM_reads_in_genes3_BAM.py /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Echinodermata/Strongylocentrotus_purpuratus-Spur_5.0/Strongylocentrotus_purpuratus-Spur_5.0.fixed.gtf Total_RNA_36hpf-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Echinodermata/Strongylocentrotus_purpuratus-Spur_5.0/Strongylocentrotus_purpuratus-Spur_5.0.chrom.sizes  sam_reads_in_genes-Total_RNA_36hpf -nomulti
python /oak/stanford/groups/akundaje/marinovg/code/transcriptome/SAM_reads_in_genes3_BAM.py /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Echinodermata/Strongylocentrotus_purpuratus-Spur_5.0/Strongylocentrotus_purpuratus-Spur_5.0.fixed.gtf Total_RNA_42hpf-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Echinodermata/Strongylocentrotus_purpuratus-Spur_5.0/Strongylocentrotus_purpuratus-Spur_5.0.chrom.sizes  sam_reads_in_genes-Total_RNA_42hpf -nomulti
python /oak/stanford/groups/akundaje/marinovg/code/transcriptome/SAM_reads_in_genes3_BAM.py /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Echinodermata/Strongylocentrotus_purpuratus-Spur_5.0/Strongylocentrotus_purpuratus-Spur_5.0.fixed.gtf Total_RNA_48hpf-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Echinodermata/Strongylocentrotus_purpuratus-Spur_5.0/Strongylocentrotus_purpuratus-Spur_5.0.chrom.sizes  sam_reads_in_genes-Total_RNA_48hpf -nomulti
python /oak/stanford/groups/akundaje/marinovg/code/transcriptome/SAM_reads_in_genes3_BAM.py /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Echinodermata/Strongylocentrotus_purpuratus-Spur_5.0/Strongylocentrotus_purpuratus-Spur_5.0.fixed.gtf Total_RNA_6hpf-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Echinodermata/Strongylocentrotus_purpuratus-Spur_5.0/Strongylocentrotus_purpuratus-Spur_5.0.chrom.sizes  sam_reads_in_genes-Total_RNA_6hpf -nomulti