python /oak/stanford/groups/akundaje/marinovg/code/transcriptome/SAM_reads_in_genes3_BAM.py /oak/stanford/groups/akundaje/marinovg/genomes/dm6/Drosophila_melanogaster.BDGP6.90.fixed.gtf Dmel01_E01h-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/dm6/dm6.chrom.sizes  sam_reads_in_genes-Dmel01_E01h -nomulti
python /oak/stanford/groups/akundaje/marinovg/code/transcriptome/SAM_reads_in_genes3_BAM.py /oak/stanford/groups/akundaje/marinovg/genomes/dm6/Drosophila_melanogaster.BDGP6.90.fixed.gtf Dmel02_E02h-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/dm6/dm6.chrom.sizes  sam_reads_in_genes-Dmel02_E02h -nomulti
python /oak/stanford/groups/akundaje/marinovg/code/transcriptome/SAM_reads_in_genes3_BAM.py /oak/stanford/groups/akundaje/marinovg/genomes/dm6/Drosophila_melanogaster.BDGP6.90.fixed.gtf Dmel03_E03h-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/dm6/dm6.chrom.sizes  sam_reads_in_genes-Dmel03_E03h -nomulti
python /oak/stanford/groups/akundaje/marinovg/code/transcriptome/SAM_reads_in_genes3_BAM.py /oak/stanford/groups/akundaje/marinovg/genomes/dm6/Drosophila_melanogaster.BDGP6.90.fixed.gtf Dmel04_E04h-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/dm6/dm6.chrom.sizes  sam_reads_in_genes-Dmel04_E04h -nomulti
python /oak/stanford/groups/akundaje/marinovg/code/transcriptome/SAM_reads_in_genes3_BAM.py /oak/stanford/groups/akundaje/marinovg/genomes/dm6/Drosophila_melanogaster.BDGP6.90.fixed.gtf Dmel05_E05h-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/dm6/dm6.chrom.sizes  sam_reads_in_genes-Dmel05_E05h -nomulti
python /oak/stanford/groups/akundaje/marinovg/code/transcriptome/SAM_reads_in_genes3_BAM.py /oak/stanford/groups/akundaje/marinovg/genomes/dm6/Drosophila_melanogaster.BDGP6.90.fixed.gtf Dmel06_E06h-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/dm6/dm6.chrom.sizes  sam_reads_in_genes-Dmel06_E06h -nomulti
python /oak/stanford/groups/akundaje/marinovg/code/transcriptome/SAM_reads_in_genes3_BAM.py /oak/stanford/groups/akundaje/marinovg/genomes/dm6/Drosophila_melanogaster.BDGP6.90.fixed.gtf Dmel07_E07h-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/dm6/dm6.chrom.sizes  sam_reads_in_genes-Dmel07_E07h -nomulti
python /oak/stanford/groups/akundaje/marinovg/code/transcriptome/SAM_reads_in_genes3_BAM.py /oak/stanford/groups/akundaje/marinovg/genomes/dm6/Drosophila_melanogaster.BDGP6.90.fixed.gtf Dmel08_E08h-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/dm6/dm6.chrom.sizes  sam_reads_in_genes-Dmel08_E08h -nomulti
python /oak/stanford/groups/akundaje/marinovg/code/transcriptome/SAM_reads_in_genes3_BAM.py /oak/stanford/groups/akundaje/marinovg/genomes/dm6/Drosophila_melanogaster.BDGP6.90.fixed.gtf Dmel09_E09h-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/dm6/dm6.chrom.sizes  sam_reads_in_genes-Dmel09_E09h -nomulti
python /oak/stanford/groups/akundaje/marinovg/code/transcriptome/SAM_reads_in_genes3_BAM.py /oak/stanford/groups/akundaje/marinovg/genomes/dm6/Drosophila_melanogaster.BDGP6.90.fixed.gtf Dmel10_E10h-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/dm6/dm6.chrom.sizes  sam_reads_in_genes-Dmel10_E10h -nomulti
python /oak/stanford/groups/akundaje/marinovg/code/transcriptome/SAM_reads_in_genes3_BAM.py /oak/stanford/groups/akundaje/marinovg/genomes/dm6/Drosophila_melanogaster.BDGP6.90.fixed.gtf Dmel11_E11h-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/dm6/dm6.chrom.sizes  sam_reads_in_genes-Dmel11_E11h -nomulti
python /oak/stanford/groups/akundaje/marinovg/code/transcriptome/SAM_reads_in_genes3_BAM.py /oak/stanford/groups/akundaje/marinovg/genomes/dm6/Drosophila_melanogaster.BDGP6.90.fixed.gtf Dmel12_E12h-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/dm6/dm6.chrom.sizes  sam_reads_in_genes-Dmel12_E12h -nomulti
python /oak/stanford/groups/akundaje/marinovg/code/transcriptome/SAM_reads_in_genes3_BAM.py /oak/stanford/groups/akundaje/marinovg/genomes/dm6/Drosophila_melanogaster.BDGP6.90.fixed.gtf Dmel13_E13h-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/dm6/dm6.chrom.sizes  sam_reads_in_genes-Dmel13_E13h -nomulti
python /oak/stanford/groups/akundaje/marinovg/code/transcriptome/SAM_reads_in_genes3_BAM.py /oak/stanford/groups/akundaje/marinovg/genomes/dm6/Drosophila_melanogaster.BDGP6.90.fixed.gtf Dmel14_E14h-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/dm6/dm6.chrom.sizes  sam_reads_in_genes-Dmel14_E14h -nomulti
python /oak/stanford/groups/akundaje/marinovg/code/transcriptome/SAM_reads_in_genes3_BAM.py /oak/stanford/groups/akundaje/marinovg/genomes/dm6/Drosophila_melanogaster.BDGP6.90.fixed.gtf Dmel15_E15h-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/dm6/dm6.chrom.sizes  sam_reads_in_genes-Dmel15_E15h -nomulti
python /oak/stanford/groups/akundaje/marinovg/code/transcriptome/SAM_reads_in_genes3_BAM.py /oak/stanford/groups/akundaje/marinovg/genomes/dm6/Drosophila_melanogaster.BDGP6.90.fixed.gtf Dmel16_E16h-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/dm6/dm6.chrom.sizes  sam_reads_in_genes-Dmel16_E16h -nomulti
python /oak/stanford/groups/akundaje/marinovg/code/transcriptome/SAM_reads_in_genes3_BAM.py /oak/stanford/groups/akundaje/marinovg/genomes/dm6/Drosophila_melanogaster.BDGP6.90.fixed.gtf Dmel17_E17h-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/dm6/dm6.chrom.sizes  sam_reads_in_genes-Dmel17_E17h -nomulti
python /oak/stanford/groups/akundaje/marinovg/code/transcriptome/SAM_reads_in_genes3_BAM.py /oak/stanford/groups/akundaje/marinovg/genomes/dm6/Drosophila_melanogaster.BDGP6.90.fixed.gtf Dmel18_E18h-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/dm6/dm6.chrom.sizes  sam_reads_in_genes-Dmel18_E18h -nomulti
python /oak/stanford/groups/akundaje/marinovg/code/transcriptome/SAM_reads_in_genes3_BAM.py /oak/stanford/groups/akundaje/marinovg/genomes/dm6/Drosophila_melanogaster.BDGP6.90.fixed.gtf Dmel19_E19h-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/dm6/dm6.chrom.sizes  sam_reads_in_genes-Dmel19_E19h -nomulti
python /oak/stanford/groups/akundaje/marinovg/code/transcriptome/SAM_reads_in_genes3_BAM.py /oak/stanford/groups/akundaje/marinovg/genomes/dm6/Drosophila_melanogaster.BDGP6.90.fixed.gtf Dmel20_E20h-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/dm6/dm6.chrom.sizes  sam_reads_in_genes-Dmel20_E20h -nomulti
python /oak/stanford/groups/akundaje/marinovg/code/transcriptome/SAM_reads_in_genes3_BAM.py /oak/stanford/groups/akundaje/marinovg/genomes/dm6/Drosophila_melanogaster.BDGP6.90.fixed.gtf Dmel21_E21h-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/dm6/dm6.chrom.sizes  sam_reads_in_genes-Dmel21_E21h -nomulti
python /oak/stanford/groups/akundaje/marinovg/code/transcriptome/SAM_reads_in_genes3_BAM.py /oak/stanford/groups/akundaje/marinovg/genomes/dm6/Drosophila_melanogaster.BDGP6.90.fixed.gtf Dmel22_E22h-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/dm6/dm6.chrom.sizes  sam_reads_in_genes-Dmel22_E22h -nomulti
python /oak/stanford/groups/akundaje/marinovg/code/transcriptome/SAM_reads_in_genes3_BAM.py /oak/stanford/groups/akundaje/marinovg/genomes/dm6/Drosophila_melanogaster.BDGP6.90.fixed.gtf Dmel23_E23h-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/dm6/dm6.chrom.sizes  sam_reads_in_genes-Dmel23_E23h -nomulti
python /oak/stanford/groups/akundaje/marinovg/code/transcriptome/SAM_reads_in_genes3_BAM.py /oak/stanford/groups/akundaje/marinovg/genomes/dm6/Drosophila_melanogaster.BDGP6.90.fixed.gtf Dmel24_E24h-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/dm6/dm6.chrom.sizes  sam_reads_in_genes-Dmel24_E24h -nomulti
python /oak/stanford/groups/akundaje/marinovg/code/transcriptome/SAM_reads_in_genes3_BAM.py /oak/stanford/groups/akundaje/marinovg/genomes/dm6/Drosophila_melanogaster.BDGP6.90.fixed.gtf Dmel25_L1-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/dm6/dm6.chrom.sizes  sam_reads_in_genes-Dmel25_L1 -nomulti
python /oak/stanford/groups/akundaje/marinovg/code/transcriptome/SAM_reads_in_genes3_BAM.py /oak/stanford/groups/akundaje/marinovg/genomes/dm6/Drosophila_melanogaster.BDGP6.90.fixed.gtf Dmel26_L2-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/dm6/dm6.chrom.sizes  sam_reads_in_genes-Dmel26_L2 -nomulti
python /oak/stanford/groups/akundaje/marinovg/code/transcriptome/SAM_reads_in_genes3_BAM.py /oak/stanford/groups/akundaje/marinovg/genomes/dm6/Drosophila_melanogaster.BDGP6.90.fixed.gtf Dmel27_L3_DG-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/dm6/dm6.chrom.sizes  sam_reads_in_genes-Dmel27_L3_DG -nomulti
python /oak/stanford/groups/akundaje/marinovg/code/transcriptome/SAM_reads_in_genes3_BAM.py /oak/stanford/groups/akundaje/marinovg/genomes/dm6/Drosophila_melanogaster.BDGP6.90.fixed.gtf Dmel28_L3_LG-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/dm6/dm6.chrom.sizes  sam_reads_in_genes-Dmel28_L3_LG -nomulti
python /oak/stanford/groups/akundaje/marinovg/code/transcriptome/SAM_reads_in_genes3_BAM.py /oak/stanford/groups/akundaje/marinovg/genomes/dm6/Drosophila_melanogaster.BDGP6.90.fixed.gtf Dmel29_L3_CG-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/dm6/dm6.chrom.sizes  sam_reads_in_genes-Dmel29_L3_CG -nomulti
python /oak/stanford/groups/akundaje/marinovg/code/transcriptome/SAM_reads_in_genes3_BAM.py /oak/stanford/groups/akundaje/marinovg/genomes/dm6/Drosophila_melanogaster.BDGP6.90.fixed.gtf Dmel30_WPP+1d-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/dm6/dm6.chrom.sizes  sam_reads_in_genes-Dmel30_WPP+1d -nomulti
python /oak/stanford/groups/akundaje/marinovg/code/transcriptome/SAM_reads_in_genes3_BAM.py /oak/stanford/groups/akundaje/marinovg/genomes/dm6/Drosophila_melanogaster.BDGP6.90.fixed.gtf Dmel31_WPP+2d-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/dm6/dm6.chrom.sizes  sam_reads_in_genes-Dmel31_WPP+2d -nomulti
python /oak/stanford/groups/akundaje/marinovg/code/transcriptome/SAM_reads_in_genes3_BAM.py /oak/stanford/groups/akundaje/marinovg/genomes/dm6/Drosophila_melanogaster.BDGP6.90.fixed.gtf Dmel32_WPP+3d-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/dm6/dm6.chrom.sizes  sam_reads_in_genes-Dmel32_WPP+3d -nomulti
python /oak/stanford/groups/akundaje/marinovg/code/transcriptome/SAM_reads_in_genes3_BAM.py /oak/stanford/groups/akundaje/marinovg/genomes/dm6/Drosophila_melanogaster.BDGP6.90.fixed.gtf Dmel33_WPP+4d-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/dm6/dm6.chrom.sizes  sam_reads_in_genes-Dmel33_WPP+4d -nomulti
python /oak/stanford/groups/akundaje/marinovg/code/transcriptome/SAM_reads_in_genes3_BAM.py /oak/stanford/groups/akundaje/marinovg/genomes/dm6/Drosophila_melanogaster.BDGP6.90.fixed.gtf Dmel34_WPP+5d-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/dm6/dm6.chrom.sizes  sam_reads_in_genes-Dmel34_WPP+5d -nomulti
python /oak/stanford/groups/akundaje/marinovg/code/transcriptome/SAM_reads_in_genes3_BAM.py /oak/stanford/groups/akundaje/marinovg/genomes/dm6/Drosophila_melanogaster.BDGP6.90.fixed.gtf Dmel35_AdM5d-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/dm6/dm6.chrom.sizes  sam_reads_in_genes-Dmel35_AdM5d -nomulti
python /oak/stanford/groups/akundaje/marinovg/code/transcriptome/SAM_reads_in_genes3_BAM.py /oak/stanford/groups/akundaje/marinovg/genomes/dm6/Drosophila_melanogaster.BDGP6.90.fixed.gtf Dmel36_AdF5d-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/dm6/dm6.chrom.sizes  sam_reads_in_genes-Dmel36_AdF5d -nomulti
python /oak/stanford/groups/akundaje/marinovg/code/transcriptome/SAM_reads_in_genes3_BAM.py /oak/stanford/groups/akundaje/marinovg/genomes/dm6/Drosophila_melanogaster.BDGP6.90.fixed.gtf Dmel_merged-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/dm6/dm6.chrom.sizes  sam_reads_in_genes-Dmel_merged -nomulti