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 Dmel2_01-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-Dmel2_01 -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 Dmel2_02-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-Dmel2_02 -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 Dmel2_03-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-Dmel2_03 -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 Dmel2_04-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-Dmel2_04 -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 Dmel2_05-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-Dmel2_05 -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 Dmel2_06-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-Dmel2_06 -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 Dmel2_07-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-Dmel2_07 -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 Dmel2_08-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-Dmel2_08 -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 Dmel2_09-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-Dmel2_09 -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 Dmel2_10-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-Dmel2_10 -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 Dmel2_11-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-Dmel2_11 -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 Dmel2_12-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-Dmel2_12 -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 Dmel2_13-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-Dmel2_13 -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 Dmel2_14-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-Dmel2_14 -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 Dmel2_15-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-Dmel2_15 -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 Dmel2_16-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-Dmel2_16 -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 Dmel2_17-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-Dmel2_17 -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 Dmel2_18-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-Dmel2_18 -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 Dmel2_19-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-Dmel2_19 -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 Dmel2_20-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-Dmel2_20 -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 Dmel2_21-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-Dmel2_21 -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 Dmel2_22-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-Dmel2_22 -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 Dmel2_23-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-Dmel2_23 -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 Dmel2_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-Dmel2_merged -nomulti