python /oak/stanford/groups/akundaje/marinovg/code/transcriptome/SAM_reads_in_genes3_BAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38/2016-11-16-refGene.gtf Quant-seq_Day-14_neuron_rep1-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes  sam_reads_in_genes-Quant-seq_Day-14_neuron_rep1 -nomulti
python /oak/stanford/groups/akundaje/marinovg/code/transcriptome/SAM_reads_in_genes3_BAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38/2016-11-16-refGene.gtf Quant-seq_Day-14_neuron_rep2-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes  sam_reads_in_genes-Quant-seq_Day-14_neuron_rep2 -nomulti
python /oak/stanford/groups/akundaje/marinovg/code/transcriptome/SAM_reads_in_genes3_BAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38/2016-11-16-refGene.gtf Quant-seq_Day-21_neuron_rep1-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes  sam_reads_in_genes-Quant-seq_Day-21_neuron_rep1 -nomulti
python /oak/stanford/groups/akundaje/marinovg/code/transcriptome/SAM_reads_in_genes3_BAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38/2016-11-16-refGene.gtf Quant-seq_Day-21_neuron_rep2-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes  sam_reads_in_genes-Quant-seq_Day-21_neuron_rep2 -nomulti
python /oak/stanford/groups/akundaje/marinovg/code/transcriptome/SAM_reads_in_genes3_BAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38/2016-11-16-refGene.gtf Quant-seq_Day-28_neuron_rep1-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes  sam_reads_in_genes-Quant-seq_Day-28_neuron_rep1 -nomulti
python /oak/stanford/groups/akundaje/marinovg/code/transcriptome/SAM_reads_in_genes3_BAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38/2016-11-16-refGene.gtf Quant-seq_Day-28_neuron_rep2-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes  sam_reads_in_genes-Quant-seq_Day-28_neuron_rep2 -nomulti