python /oak/stanford/groups/akundaje/marinovg/code/transcriptome/SAM_reads_in_genes3_BAM.py /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Insects/Drosophila_erecta/Drosophila_erecta.dere_caf1.20.gtf Dere_01-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Insects/Drosophila_erecta/Drosophila_erecta.dere_caf1.20.chrom.sizes  sam_reads_in_genes-Dere_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_erecta/Drosophila_erecta.dere_caf1.20.gtf Dere_02-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Insects/Drosophila_erecta/Drosophila_erecta.dere_caf1.20.chrom.sizes  sam_reads_in_genes-Dere_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_erecta/Drosophila_erecta.dere_caf1.20.gtf Dere_03-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Insects/Drosophila_erecta/Drosophila_erecta.dere_caf1.20.chrom.sizes  sam_reads_in_genes-Dere_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_erecta/Drosophila_erecta.dere_caf1.20.gtf Dere_04-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Insects/Drosophila_erecta/Drosophila_erecta.dere_caf1.20.chrom.sizes  sam_reads_in_genes-Dere_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_erecta/Drosophila_erecta.dere_caf1.20.gtf Dere_05-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Insects/Drosophila_erecta/Drosophila_erecta.dere_caf1.20.chrom.sizes  sam_reads_in_genes-Dere_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_erecta/Drosophila_erecta.dere_caf1.20.gtf Dere_06-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Insects/Drosophila_erecta/Drosophila_erecta.dere_caf1.20.chrom.sizes  sam_reads_in_genes-Dere_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_erecta/Drosophila_erecta.dere_caf1.20.gtf Dere_07-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Insects/Drosophila_erecta/Drosophila_erecta.dere_caf1.20.chrom.sizes  sam_reads_in_genes-Dere_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_erecta/Drosophila_erecta.dere_caf1.20.gtf Dere_08-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Insects/Drosophila_erecta/Drosophila_erecta.dere_caf1.20.chrom.sizes  sam_reads_in_genes-Dere_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_erecta/Drosophila_erecta.dere_caf1.20.gtf Dere_09-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Insects/Drosophila_erecta/Drosophila_erecta.dere_caf1.20.chrom.sizes  sam_reads_in_genes-Dere_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_erecta/Drosophila_erecta.dere_caf1.20.gtf Dere_10-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Insects/Drosophila_erecta/Drosophila_erecta.dere_caf1.20.chrom.sizes  sam_reads_in_genes-Dere_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_erecta/Drosophila_erecta.dere_caf1.20.gtf Dere_11-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Insects/Drosophila_erecta/Drosophila_erecta.dere_caf1.20.chrom.sizes  sam_reads_in_genes-Dere_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_erecta/Drosophila_erecta.dere_caf1.20.gtf Dere_12-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Insects/Drosophila_erecta/Drosophila_erecta.dere_caf1.20.chrom.sizes  sam_reads_in_genes-Dere_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_erecta/Drosophila_erecta.dere_caf1.20.gtf Dere_13-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Insects/Drosophila_erecta/Drosophila_erecta.dere_caf1.20.chrom.sizes  sam_reads_in_genes-Dere_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_erecta/Drosophila_erecta.dere_caf1.20.gtf Dere_14-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Insects/Drosophila_erecta/Drosophila_erecta.dere_caf1.20.chrom.sizes  sam_reads_in_genes-Dere_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_erecta/Drosophila_erecta.dere_caf1.20.gtf Dere_15-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Insects/Drosophila_erecta/Drosophila_erecta.dere_caf1.20.chrom.sizes  sam_reads_in_genes-Dere_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_erecta/Drosophila_erecta.dere_caf1.20.gtf Dere_16-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Insects/Drosophila_erecta/Drosophila_erecta.dere_caf1.20.chrom.sizes  sam_reads_in_genes-Dere_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_erecta/Drosophila_erecta.dere_caf1.20.gtf Dere_17-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Insects/Drosophila_erecta/Drosophila_erecta.dere_caf1.20.chrom.sizes  sam_reads_in_genes-Dere_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_erecta/Drosophila_erecta.dere_caf1.20.gtf Dere_18-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Insects/Drosophila_erecta/Drosophila_erecta.dere_caf1.20.chrom.sizes  sam_reads_in_genes-Dere_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_erecta/Drosophila_erecta.dere_caf1.20.gtf Dere_19-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Insects/Drosophila_erecta/Drosophila_erecta.dere_caf1.20.chrom.sizes  sam_reads_in_genes-Dere_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_erecta/Drosophila_erecta.dere_caf1.20.gtf Dere_20-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Insects/Drosophila_erecta/Drosophila_erecta.dere_caf1.20.chrom.sizes  sam_reads_in_genes-Dere_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_erecta/Drosophila_erecta.dere_caf1.20.gtf Dere_21-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Insects/Drosophila_erecta/Drosophila_erecta.dere_caf1.20.chrom.sizes  sam_reads_in_genes-Dere_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_erecta/Drosophila_erecta.dere_caf1.20.gtf Dere_22-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Insects/Drosophila_erecta/Drosophila_erecta.dere_caf1.20.chrom.sizes  sam_reads_in_genes-Dere_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_erecta/Drosophila_erecta.dere_caf1.20.gtf Dere_23-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Insects/Drosophila_erecta/Drosophila_erecta.dere_caf1.20.chrom.sizes  sam_reads_in_genes-Dere_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_erecta/Drosophila_erecta.dere_caf1.20.gtf Dere_merged-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Insects/Drosophila_erecta/Drosophila_erecta.dere_caf1.20.chrom.sizes  sam_reads_in_genes-Dere_merged -nomulti