python /oak/stanford/groups/akundaje/marinovg/code/transcriptome/SAM_reads_in_genes3_BAM.py /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Fishes/danRer11/Danio_rerio.GRCz11.102.fixed.gtf WT_12hpf-GSM3141415-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Fishes/danRer11/danRer11_no_alt.chrom.sizes  sam_reads_in_genes-WT_12hpf-GSM3141415 -nomulti
python /oak/stanford/groups/akundaje/marinovg/code/transcriptome/SAM_reads_in_genes3_BAM.py /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Fishes/danRer11/Danio_rerio.GRCz11.102.fixed.gtf WT_12hpf_2-GSM4144776-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Fishes/danRer11/danRer11_no_alt.chrom.sizes  sam_reads_in_genes-WT_12hpf_2-GSM4144776 -nomulti
python /oak/stanford/groups/akundaje/marinovg/code/transcriptome/SAM_reads_in_genes3_BAM.py /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Fishes/danRer11/Danio_rerio.GRCz11.102.fixed.gtf WT_16hpf-GSM3141416-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Fishes/danRer11/danRer11_no_alt.chrom.sizes  sam_reads_in_genes-WT_16hpf-GSM3141416 -nomulti
python /oak/stanford/groups/akundaje/marinovg/code/transcriptome/SAM_reads_in_genes3_BAM.py /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Fishes/danRer11/Danio_rerio.GRCz11.102.fixed.gtf WT_16hpf_2-GSM4144777-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Fishes/danRer11/danRer11_no_alt.chrom.sizes  sam_reads_in_genes-WT_16hpf_2-GSM4144777 -nomulti
python /oak/stanford/groups/akundaje/marinovg/code/transcriptome/SAM_reads_in_genes3_BAM.py /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Fishes/danRer11/Danio_rerio.GRCz11.102.fixed.gtf sa37_12hpf-GSM3141417-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Fishes/danRer11/danRer11_no_alt.chrom.sizes  sam_reads_in_genes-sa37_12hpf-GSM3141417 -nomulti
python /oak/stanford/groups/akundaje/marinovg/code/transcriptome/SAM_reads_in_genes3_BAM.py /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Fishes/danRer11/Danio_rerio.GRCz11.102.fixed.gtf sa37_12hpf_2-GSM4144778-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Fishes/danRer11/danRer11_no_alt.chrom.sizes  sam_reads_in_genes-sa37_12hpf_2-GSM4144778 -nomulti
python /oak/stanford/groups/akundaje/marinovg/code/transcriptome/SAM_reads_in_genes3_BAM.py /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Fishes/danRer11/Danio_rerio.GRCz11.102.fixed.gtf sa37_16hpf-GSM3141418-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Fishes/danRer11/danRer11_no_alt.chrom.sizes  sam_reads_in_genes-sa37_16hpf-GSM3141418 -nomulti
python /oak/stanford/groups/akundaje/marinovg/code/transcriptome/SAM_reads_in_genes3_BAM.py /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Fishes/danRer11/Danio_rerio.GRCz11.102.fixed.gtf sa37_16hpf_2-GSM4144779-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Fishes/danRer11/danRer11_no_alt.chrom.sizes  sam_reads_in_genes-sa37_16hpf_2-GSM4144779 -nomulti