python /oak/stanford/groups/akundaje/marinovg/code/transcriptome/SAM_reads_in_genes3_BAM.py /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Insects/Drosophila_simulans/Drosophila_simulans.WUGSC1.20.fixed.gtf Dsim_01-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Insects/Drosophila_simulans/Drosophila_simulans.WUGSC1.20.chrom.sizes  sam_reads_in_genes-Dsim_01 -nomulti
python /oak/stanford/groups/akundaje/marinovg/code/transcriptome/SAM_reads_in_genes3_BAM.py /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Insects/Drosophila_simulans/Drosophila_simulans.WUGSC1.20.fixed.gtf Dsim_02-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Insects/Drosophila_simulans/Drosophila_simulans.WUGSC1.20.chrom.sizes  sam_reads_in_genes-Dsim_02 -nomulti
python /oak/stanford/groups/akundaje/marinovg/code/transcriptome/SAM_reads_in_genes3_BAM.py /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Insects/Drosophila_simulans/Drosophila_simulans.WUGSC1.20.fixed.gtf Dsim_03-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Insects/Drosophila_simulans/Drosophila_simulans.WUGSC1.20.chrom.sizes  sam_reads_in_genes-Dsim_03 -nomulti
python /oak/stanford/groups/akundaje/marinovg/code/transcriptome/SAM_reads_in_genes3_BAM.py /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Insects/Drosophila_simulans/Drosophila_simulans.WUGSC1.20.fixed.gtf Dsim_04-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Insects/Drosophila_simulans/Drosophila_simulans.WUGSC1.20.chrom.sizes  sam_reads_in_genes-Dsim_04 -nomulti
python /oak/stanford/groups/akundaje/marinovg/code/transcriptome/SAM_reads_in_genes3_BAM.py /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Insects/Drosophila_simulans/Drosophila_simulans.WUGSC1.20.fixed.gtf Dsim_05-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Insects/Drosophila_simulans/Drosophila_simulans.WUGSC1.20.chrom.sizes  sam_reads_in_genes-Dsim_05 -nomulti
python /oak/stanford/groups/akundaje/marinovg/code/transcriptome/SAM_reads_in_genes3_BAM.py /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Insects/Drosophila_simulans/Drosophila_simulans.WUGSC1.20.fixed.gtf Dsim_06-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Insects/Drosophila_simulans/Drosophila_simulans.WUGSC1.20.chrom.sizes  sam_reads_in_genes-Dsim_06 -nomulti
python /oak/stanford/groups/akundaje/marinovg/code/transcriptome/SAM_reads_in_genes3_BAM.py /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Insects/Drosophila_simulans/Drosophila_simulans.WUGSC1.20.fixed.gtf Dsim_07-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Insects/Drosophila_simulans/Drosophila_simulans.WUGSC1.20.chrom.sizes  sam_reads_in_genes-Dsim_07 -nomulti
python /oak/stanford/groups/akundaje/marinovg/code/transcriptome/SAM_reads_in_genes3_BAM.py /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Insects/Drosophila_simulans/Drosophila_simulans.WUGSC1.20.fixed.gtf Dsim_08-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Insects/Drosophila_simulans/Drosophila_simulans.WUGSC1.20.chrom.sizes  sam_reads_in_genes-Dsim_08 -nomulti
python /oak/stanford/groups/akundaje/marinovg/code/transcriptome/SAM_reads_in_genes3_BAM.py /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Insects/Drosophila_simulans/Drosophila_simulans.WUGSC1.20.fixed.gtf Dsim_09-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Insects/Drosophila_simulans/Drosophila_simulans.WUGSC1.20.chrom.sizes  sam_reads_in_genes-Dsim_09 -nomulti
python /oak/stanford/groups/akundaje/marinovg/code/transcriptome/SAM_reads_in_genes3_BAM.py /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Insects/Drosophila_simulans/Drosophila_simulans.WUGSC1.20.fixed.gtf Dsim_10-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Insects/Drosophila_simulans/Drosophila_simulans.WUGSC1.20.chrom.sizes  sam_reads_in_genes-Dsim_10 -nomulti
python /oak/stanford/groups/akundaje/marinovg/code/transcriptome/SAM_reads_in_genes3_BAM.py /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Insects/Drosophila_simulans/Drosophila_simulans.WUGSC1.20.fixed.gtf Dsim_11-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Insects/Drosophila_simulans/Drosophila_simulans.WUGSC1.20.chrom.sizes  sam_reads_in_genes-Dsim_11 -nomulti
python /oak/stanford/groups/akundaje/marinovg/code/transcriptome/SAM_reads_in_genes3_BAM.py /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Insects/Drosophila_simulans/Drosophila_simulans.WUGSC1.20.fixed.gtf Dsim_12-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Insects/Drosophila_simulans/Drosophila_simulans.WUGSC1.20.chrom.sizes  sam_reads_in_genes-Dsim_12 -nomulti
python /oak/stanford/groups/akundaje/marinovg/code/transcriptome/SAM_reads_in_genes3_BAM.py /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Insects/Drosophila_simulans/Drosophila_simulans.WUGSC1.20.fixed.gtf Dsim_13-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Insects/Drosophila_simulans/Drosophila_simulans.WUGSC1.20.chrom.sizes  sam_reads_in_genes-Dsim_13 -nomulti
python /oak/stanford/groups/akundaje/marinovg/code/transcriptome/SAM_reads_in_genes3_BAM.py /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Insects/Drosophila_simulans/Drosophila_simulans.WUGSC1.20.fixed.gtf Dsim_14-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Insects/Drosophila_simulans/Drosophila_simulans.WUGSC1.20.chrom.sizes  sam_reads_in_genes-Dsim_14 -nomulti
python /oak/stanford/groups/akundaje/marinovg/code/transcriptome/SAM_reads_in_genes3_BAM.py /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Insects/Drosophila_simulans/Drosophila_simulans.WUGSC1.20.fixed.gtf Dsim_15-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Insects/Drosophila_simulans/Drosophila_simulans.WUGSC1.20.chrom.sizes  sam_reads_in_genes-Dsim_15 -nomulti
python /oak/stanford/groups/akundaje/marinovg/code/transcriptome/SAM_reads_in_genes3_BAM.py /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Insects/Drosophila_simulans/Drosophila_simulans.WUGSC1.20.fixed.gtf Dsim_16-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Insects/Drosophila_simulans/Drosophila_simulans.WUGSC1.20.chrom.sizes  sam_reads_in_genes-Dsim_16 -nomulti
python /oak/stanford/groups/akundaje/marinovg/code/transcriptome/SAM_reads_in_genes3_BAM.py /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Insects/Drosophila_simulans/Drosophila_simulans.WUGSC1.20.fixed.gtf Dsim_17-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Insects/Drosophila_simulans/Drosophila_simulans.WUGSC1.20.chrom.sizes  sam_reads_in_genes-Dsim_17 -nomulti
python /oak/stanford/groups/akundaje/marinovg/code/transcriptome/SAM_reads_in_genes3_BAM.py /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Insects/Drosophila_simulans/Drosophila_simulans.WUGSC1.20.fixed.gtf Dsim_18-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Insects/Drosophila_simulans/Drosophila_simulans.WUGSC1.20.chrom.sizes  sam_reads_in_genes-Dsim_18 -nomulti
python /oak/stanford/groups/akundaje/marinovg/code/transcriptome/SAM_reads_in_genes3_BAM.py /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Insects/Drosophila_simulans/Drosophila_simulans.WUGSC1.20.fixed.gtf Dsim_19-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Insects/Drosophila_simulans/Drosophila_simulans.WUGSC1.20.chrom.sizes  sam_reads_in_genes-Dsim_19 -nomulti
python /oak/stanford/groups/akundaje/marinovg/code/transcriptome/SAM_reads_in_genes3_BAM.py /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Insects/Drosophila_simulans/Drosophila_simulans.WUGSC1.20.fixed.gtf Dsim_20-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Insects/Drosophila_simulans/Drosophila_simulans.WUGSC1.20.chrom.sizes  sam_reads_in_genes-Dsim_20 -nomulti
python /oak/stanford/groups/akundaje/marinovg/code/transcriptome/SAM_reads_in_genes3_BAM.py /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Insects/Drosophila_simulans/Drosophila_simulans.WUGSC1.20.fixed.gtf Dsim_21-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Insects/Drosophila_simulans/Drosophila_simulans.WUGSC1.20.chrom.sizes  sam_reads_in_genes-Dsim_21 -nomulti
python /oak/stanford/groups/akundaje/marinovg/code/transcriptome/SAM_reads_in_genes3_BAM.py /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Insects/Drosophila_simulans/Drosophila_simulans.WUGSC1.20.fixed.gtf Dsim_22-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Insects/Drosophila_simulans/Drosophila_simulans.WUGSC1.20.chrom.sizes  sam_reads_in_genes-Dsim_22 -nomulti
python /oak/stanford/groups/akundaje/marinovg/code/transcriptome/SAM_reads_in_genes3_BAM.py /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Insects/Drosophila_simulans/Drosophila_simulans.WUGSC1.20.fixed.gtf Dsim_merged-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Insects/Drosophila_simulans/Drosophila_simulans.WUGSC1.20.chrom.sizes  sam_reads_in_genes-Dsim_merged -nomulti