python /oak/stanford/groups/akundaje/marinovg/code/transcriptome/SAM_reads_in_genes3_BAM.py /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Insects/Locusta_migratoria-LocustGenomeV1/Gallus_gallus.GRCg6a.102.gtf Antenna-rep1-SRR11929153-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Insects/Locusta_migratoria-LocustGenomeV1/GCA_000516895.1_LocustGenomeV1_genomic.chrom.sizes  sam_reads_in_genes-Antenna-rep1-SRR11929153 -nomulti
python /oak/stanford/groups/akundaje/marinovg/code/transcriptome/SAM_reads_in_genes3_BAM.py /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Insects/Locusta_migratoria-LocustGenomeV1/Gallus_gallus.GRCg6a.102.gtf Brain-rep1-SRR11929152-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Insects/Locusta_migratoria-LocustGenomeV1/GCA_000516895.1_LocustGenomeV1_genomic.chrom.sizes  sam_reads_in_genes-Brain-rep1-SRR11929152 -nomulti
python /oak/stanford/groups/akundaje/marinovg/code/transcriptome/SAM_reads_in_genes3_BAM.py /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Insects/Locusta_migratoria-LocustGenomeV1/Gallus_gallus.GRCg6a.102.gtf Fatbody-rep1-SRR11929147-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Insects/Locusta_migratoria-LocustGenomeV1/GCA_000516895.1_LocustGenomeV1_genomic.chrom.sizes  sam_reads_in_genes-Fatbody-rep1-SRR11929147 -nomulti
python /oak/stanford/groups/akundaje/marinovg/code/transcriptome/SAM_reads_in_genes3_BAM.py /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Insects/Locusta_migratoria-LocustGenomeV1/Gallus_gallus.GRCg6a.102.gtf Labipalp-rep1-SRR11929146-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Insects/Locusta_migratoria-LocustGenomeV1/GCA_000516895.1_LocustGenomeV1_genomic.chrom.sizes  sam_reads_in_genes-Labipalp-rep1-SRR11929146 -nomulti
python /oak/stanford/groups/akundaje/marinovg/code/transcriptome/SAM_reads_in_genes3_BAM.py /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Insects/Locusta_migratoria-LocustGenomeV1/Gallus_gallus.GRCg6a.102.gtf Labipalp-rep2-SRR11929145-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Insects/Locusta_migratoria-LocustGenomeV1/GCA_000516895.1_LocustGenomeV1_genomic.chrom.sizes  sam_reads_in_genes-Labipalp-rep2-SRR11929145 -nomulti
python /oak/stanford/groups/akundaje/marinovg/code/transcriptome/SAM_reads_in_genes3_BAM.py /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Insects/Locusta_migratoria-LocustGenomeV1/Gallus_gallus.GRCg6a.102.gtf Ovary-rep1-SRR11929144-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Insects/Locusta_migratoria-LocustGenomeV1/GCA_000516895.1_LocustGenomeV1_genomic.chrom.sizes  sam_reads_in_genes-Ovary-rep1-SRR11929144 -nomulti
python /oak/stanford/groups/akundaje/marinovg/code/transcriptome/SAM_reads_in_genes3_BAM.py /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Insects/Locusta_migratoria-LocustGenomeV1/Gallus_gallus.GRCg6a.102.gtf Pronotum-rep1-SRR11929143-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Insects/Locusta_migratoria-LocustGenomeV1/GCA_000516895.1_LocustGenomeV1_genomic.chrom.sizes  sam_reads_in_genes-Pronotum-rep1-SRR11929143 -nomulti
python /oak/stanford/groups/akundaje/marinovg/code/transcriptome/SAM_reads_in_genes3_BAM.py /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Insects/Locusta_migratoria-LocustGenomeV1/Gallus_gallus.GRCg6a.102.gtf Pronotum-rep2-SRR11929142-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Insects/Locusta_migratoria-LocustGenomeV1/GCA_000516895.1_LocustGenomeV1_genomic.chrom.sizes  sam_reads_in_genes-Pronotum-rep2-SRR11929142 -nomulti
python /oak/stanford/groups/akundaje/marinovg/code/transcriptome/SAM_reads_in_genes3_BAM.py /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Insects/Locusta_migratoria-LocustGenomeV1/Gallus_gallus.GRCg6a.102.gtf Testis-rep1-SRR11929141-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Insects/Locusta_migratoria-LocustGenomeV1/GCA_000516895.1_LocustGenomeV1_genomic.chrom.sizes  sam_reads_in_genes-Testis-rep1-SRR11929141 -nomulti
python /oak/stanford/groups/akundaje/marinovg/code/transcriptome/SAM_reads_in_genes3_BAM.py /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Insects/Locusta_migratoria-LocustGenomeV1/Gallus_gallus.GRCg6a.102.gtf Testis-rep2-SRR11929140-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Insects/Locusta_migratoria-LocustGenomeV1/GCA_000516895.1_LocustGenomeV1_genomic.chrom.sizes  sam_reads_in_genes-Testis-rep2-SRR11929140 -nomulti
python /oak/stanford/groups/akundaje/marinovg/code/transcriptome/SAM_reads_in_genes3_BAM.py /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Insects/Locusta_migratoria-LocustGenomeV1/Gallus_gallus.GRCg6a.102.gtf Thoracic_muscle-rep1-SRR11929151-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Insects/Locusta_migratoria-LocustGenomeV1/GCA_000516895.1_LocustGenomeV1_genomic.chrom.sizes  sam_reads_in_genes-Thoracic_muscle-rep1-SRR11929151 -nomulti
python /oak/stanford/groups/akundaje/marinovg/code/transcriptome/SAM_reads_in_genes3_BAM.py /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Insects/Locusta_migratoria-LocustGenomeV1/Gallus_gallus.GRCg6a.102.gtf Thoracic_muscle-rep2-SRR11929150-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Insects/Locusta_migratoria-LocustGenomeV1/GCA_000516895.1_LocustGenomeV1_genomic.chrom.sizes  sam_reads_in_genes-Thoracic_muscle-rep2-SRR11929150 -nomulti
python /oak/stanford/groups/akundaje/marinovg/code/transcriptome/SAM_reads_in_genes3_BAM.py /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Insects/Locusta_migratoria-LocustGenomeV1/Gallus_gallus.GRCg6a.102.gtf Wing-rep1-SRR11929149-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Insects/Locusta_migratoria-LocustGenomeV1/GCA_000516895.1_LocustGenomeV1_genomic.chrom.sizes  sam_reads_in_genes-Wing-rep1-SRR11929149 -nomulti
python /oak/stanford/groups/akundaje/marinovg/code/transcriptome/SAM_reads_in_genes3_BAM.py /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Insects/Locusta_migratoria-LocustGenomeV1/Gallus_gallus.GRCg6a.102.gtf Wing-rep2-SRR11929148-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Insects/Locusta_migratoria-LocustGenomeV1/GCA_000516895.1_LocustGenomeV1_genomic.chrom.sizes  sam_reads_in_genes-Wing-rep2-SRR11929148 -nomulti