python /oak/stanford/groups/akundaje/marinovg/code/transcriptome/SAM_reads_in_genes3_BAM.py /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Insects/Drosophila_pseudoobscura/Drosophila_pseudoobscura.HGSC2.20.fixed.gtf Dpse_01-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Insects/Drosophila_pseudoobscura/Drosophila_pseudoobscura.HGSC2.20.chrom.sizes  sam_reads_in_genes-Dpse_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_pseudoobscura/Drosophila_pseudoobscura.HGSC2.20.fixed.gtf Dpse_02-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Insects/Drosophila_pseudoobscura/Drosophila_pseudoobscura.HGSC2.20.chrom.sizes  sam_reads_in_genes-Dpse_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_pseudoobscura/Drosophila_pseudoobscura.HGSC2.20.fixed.gtf Dpse_03-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Insects/Drosophila_pseudoobscura/Drosophila_pseudoobscura.HGSC2.20.chrom.sizes  sam_reads_in_genes-Dpse_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_pseudoobscura/Drosophila_pseudoobscura.HGSC2.20.fixed.gtf Dpse_04-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Insects/Drosophila_pseudoobscura/Drosophila_pseudoobscura.HGSC2.20.chrom.sizes  sam_reads_in_genes-Dpse_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_pseudoobscura/Drosophila_pseudoobscura.HGSC2.20.fixed.gtf Dpse_05-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Insects/Drosophila_pseudoobscura/Drosophila_pseudoobscura.HGSC2.20.chrom.sizes  sam_reads_in_genes-Dpse_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_pseudoobscura/Drosophila_pseudoobscura.HGSC2.20.fixed.gtf Dpse_06-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Insects/Drosophila_pseudoobscura/Drosophila_pseudoobscura.HGSC2.20.chrom.sizes  sam_reads_in_genes-Dpse_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_pseudoobscura/Drosophila_pseudoobscura.HGSC2.20.fixed.gtf Dpse_07-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Insects/Drosophila_pseudoobscura/Drosophila_pseudoobscura.HGSC2.20.chrom.sizes  sam_reads_in_genes-Dpse_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_pseudoobscura/Drosophila_pseudoobscura.HGSC2.20.fixed.gtf Dpse_08-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Insects/Drosophila_pseudoobscura/Drosophila_pseudoobscura.HGSC2.20.chrom.sizes  sam_reads_in_genes-Dpse_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_pseudoobscura/Drosophila_pseudoobscura.HGSC2.20.fixed.gtf Dpse_09-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Insects/Drosophila_pseudoobscura/Drosophila_pseudoobscura.HGSC2.20.chrom.sizes  sam_reads_in_genes-Dpse_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_pseudoobscura/Drosophila_pseudoobscura.HGSC2.20.fixed.gtf Dpse_10-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Insects/Drosophila_pseudoobscura/Drosophila_pseudoobscura.HGSC2.20.chrom.sizes  sam_reads_in_genes-Dpse_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_pseudoobscura/Drosophila_pseudoobscura.HGSC2.20.fixed.gtf Dpse_11-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Insects/Drosophila_pseudoobscura/Drosophila_pseudoobscura.HGSC2.20.chrom.sizes  sam_reads_in_genes-Dpse_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_pseudoobscura/Drosophila_pseudoobscura.HGSC2.20.fixed.gtf Dpse_12-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Insects/Drosophila_pseudoobscura/Drosophila_pseudoobscura.HGSC2.20.chrom.sizes  sam_reads_in_genes-Dpse_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_pseudoobscura/Drosophila_pseudoobscura.HGSC2.20.fixed.gtf Dpse_13-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Insects/Drosophila_pseudoobscura/Drosophila_pseudoobscura.HGSC2.20.chrom.sizes  sam_reads_in_genes-Dpse_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_pseudoobscura/Drosophila_pseudoobscura.HGSC2.20.fixed.gtf Dpse_14-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Insects/Drosophila_pseudoobscura/Drosophila_pseudoobscura.HGSC2.20.chrom.sizes  sam_reads_in_genes-Dpse_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_pseudoobscura/Drosophila_pseudoobscura.HGSC2.20.fixed.gtf Dpse_15-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Insects/Drosophila_pseudoobscura/Drosophila_pseudoobscura.HGSC2.20.chrom.sizes  sam_reads_in_genes-Dpse_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_pseudoobscura/Drosophila_pseudoobscura.HGSC2.20.fixed.gtf Dpse_16-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Insects/Drosophila_pseudoobscura/Drosophila_pseudoobscura.HGSC2.20.chrom.sizes  sam_reads_in_genes-Dpse_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_pseudoobscura/Drosophila_pseudoobscura.HGSC2.20.fixed.gtf Dpse_17-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Insects/Drosophila_pseudoobscura/Drosophila_pseudoobscura.HGSC2.20.chrom.sizes  sam_reads_in_genes-Dpse_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_pseudoobscura/Drosophila_pseudoobscura.HGSC2.20.fixed.gtf Dpse_18-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Insects/Drosophila_pseudoobscura/Drosophila_pseudoobscura.HGSC2.20.chrom.sizes  sam_reads_in_genes-Dpse_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_pseudoobscura/Drosophila_pseudoobscura.HGSC2.20.fixed.gtf Dpse_19-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Insects/Drosophila_pseudoobscura/Drosophila_pseudoobscura.HGSC2.20.chrom.sizes  sam_reads_in_genes-Dpse_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_pseudoobscura/Drosophila_pseudoobscura.HGSC2.20.fixed.gtf Dpse_20-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Insects/Drosophila_pseudoobscura/Drosophila_pseudoobscura.HGSC2.20.chrom.sizes  sam_reads_in_genes-Dpse_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_pseudoobscura/Drosophila_pseudoobscura.HGSC2.20.fixed.gtf Dpse_21-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Insects/Drosophila_pseudoobscura/Drosophila_pseudoobscura.HGSC2.20.chrom.sizes  sam_reads_in_genes-Dpse_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_pseudoobscura/Drosophila_pseudoobscura.HGSC2.20.fixed.gtf Dpse_22-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Insects/Drosophila_pseudoobscura/Drosophila_pseudoobscura.HGSC2.20.chrom.sizes  sam_reads_in_genes-Dpse_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_pseudoobscura/Drosophila_pseudoobscura.HGSC2.20.fixed.gtf Dpse_23-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Insects/Drosophila_pseudoobscura/Drosophila_pseudoobscura.HGSC2.20.chrom.sizes  sam_reads_in_genes-Dpse_23 -nomulti
python /oak/stanford/groups/akundaje/marinovg/code/transcriptome/SAM_reads_in_genes3_BAM.py /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Insects/Drosophila_pseudoobscura/Drosophila_pseudoobscura.HGSC2.20.fixed.gtf Dpse_24-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Insects/Drosophila_pseudoobscura/Drosophila_pseudoobscura.HGSC2.20.chrom.sizes  sam_reads_in_genes-Dpse_24 -nomulti
python /oak/stanford/groups/akundaje/marinovg/code/transcriptome/SAM_reads_in_genes3_BAM.py /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Insects/Drosophila_pseudoobscura/Drosophila_pseudoobscura.HGSC2.20.fixed.gtf Dpse_25-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Insects/Drosophila_pseudoobscura/Drosophila_pseudoobscura.HGSC2.20.chrom.sizes  sam_reads_in_genes-Dpse_25 -nomulti
python /oak/stanford/groups/akundaje/marinovg/code/transcriptome/SAM_reads_in_genes3_BAM.py /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Insects/Drosophila_pseudoobscura/Drosophila_pseudoobscura.HGSC2.20.fixed.gtf Dpse_26-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Insects/Drosophila_pseudoobscura/Drosophila_pseudoobscura.HGSC2.20.chrom.sizes  sam_reads_in_genes-Dpse_26 -nomulti
python /oak/stanford/groups/akundaje/marinovg/code/transcriptome/SAM_reads_in_genes3_BAM.py /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Insects/Drosophila_pseudoobscura/Drosophila_pseudoobscura.HGSC2.20.fixed.gtf Dpse_27-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Insects/Drosophila_pseudoobscura/Drosophila_pseudoobscura.HGSC2.20.chrom.sizes  sam_reads_in_genes-Dpse_27 -nomulti
python /oak/stanford/groups/akundaje/marinovg/code/transcriptome/SAM_reads_in_genes3_BAM.py /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Insects/Drosophila_pseudoobscura/Drosophila_pseudoobscura.HGSC2.20.fixed.gtf Dpse_28-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Insects/Drosophila_pseudoobscura/Drosophila_pseudoobscura.HGSC2.20.chrom.sizes  sam_reads_in_genes-Dpse_28 -nomulti
python /oak/stanford/groups/akundaje/marinovg/code/transcriptome/SAM_reads_in_genes3_BAM.py /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Insects/Drosophila_pseudoobscura/Drosophila_pseudoobscura.HGSC2.20.fixed.gtf Dpse_29-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Insects/Drosophila_pseudoobscura/Drosophila_pseudoobscura.HGSC2.20.chrom.sizes  sam_reads_in_genes-Dpse_29 -nomulti
python /oak/stanford/groups/akundaje/marinovg/code/transcriptome/SAM_reads_in_genes3_BAM.py /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Insects/Drosophila_pseudoobscura/Drosophila_pseudoobscura.HGSC2.20.fixed.gtf Dpse_merged-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Insects/Drosophila_pseudoobscura/Drosophila_pseudoobscura.HGSC2.20.chrom.sizes  sam_reads_in_genes-Dpse_merged -nomulti