python /oak/stanford/groups/akundaje/marinovg/code/transcriptome/SAM_reads_in_genes3_BAM.py /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Bos_taurus-ARS-UCD1.2/Bos_taurus.ARS-UCD1.2.102.gtf Abomasum-pooled-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Bos_taurus-ARS-UCD1.2/Bos_taurus.ARS-UCD1.2.dna.toplevel.chrom.sizes  sam_reads_in_genes-Abomasum-pooled -nomulti
python /oak/stanford/groups/akundaje/marinovg/code/transcriptome/SAM_reads_in_genes3_BAM.py /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Bos_taurus-ARS-UCD1.2/Bos_taurus.ARS-UCD1.2.102.gtf Adipose-pooled-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Bos_taurus-ARS-UCD1.2/Bos_taurus.ARS-UCD1.2.dna.toplevel.chrom.sizes  sam_reads_in_genes-Adipose-pooled -nomulti
python /oak/stanford/groups/akundaje/marinovg/code/transcriptome/SAM_reads_in_genes3_BAM.py /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Bos_taurus-ARS-UCD1.2/Bos_taurus.ARS-UCD1.2.102.gtf Bladder-pooled-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Bos_taurus-ARS-UCD1.2/Bos_taurus.ARS-UCD1.2.dna.toplevel.chrom.sizes  sam_reads_in_genes-Bladder-pooled -nomulti
python /oak/stanford/groups/akundaje/marinovg/code/transcriptome/SAM_reads_in_genes3_BAM.py /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Bos_taurus-ARS-UCD1.2/Bos_taurus.ARS-UCD1.2.102.gtf BoneMarrow-pooled-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Bos_taurus-ARS-UCD1.2/Bos_taurus.ARS-UCD1.2.dna.toplevel.chrom.sizes  sam_reads_in_genes-BoneMarrow-pooled -nomulti
python /oak/stanford/groups/akundaje/marinovg/code/transcriptome/SAM_reads_in_genes3_BAM.py /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Bos_taurus-ARS-UCD1.2/Bos_taurus.ARS-UCD1.2.102.gtf BrainCortex-pooled-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Bos_taurus-ARS-UCD1.2/Bos_taurus.ARS-UCD1.2.dna.toplevel.chrom.sizes  sam_reads_in_genes-BrainCortex-pooled -nomulti
python /oak/stanford/groups/akundaje/marinovg/code/transcriptome/SAM_reads_in_genes3_BAM.py /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Bos_taurus-ARS-UCD1.2/Bos_taurus.ARS-UCD1.2.102.gtf Cecum-pooled-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Bos_taurus-ARS-UCD1.2/Bos_taurus.ARS-UCD1.2.dna.toplevel.chrom.sizes  sam_reads_in_genes-Cecum-pooled -nomulti
python /oak/stanford/groups/akundaje/marinovg/code/transcriptome/SAM_reads_in_genes3_BAM.py /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Bos_taurus-ARS-UCD1.2/Bos_taurus.ARS-UCD1.2.102.gtf Cerebellum-pooled-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Bos_taurus-ARS-UCD1.2/Bos_taurus.ARS-UCD1.2.dna.toplevel.chrom.sizes  sam_reads_in_genes-Cerebellum-pooled -nomulti
python /oak/stanford/groups/akundaje/marinovg/code/transcriptome/SAM_reads_in_genes3_BAM.py /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Bos_taurus-ARS-UCD1.2/Bos_taurus.ARS-UCD1.2.102.gtf Colon-pooled-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Bos_taurus-ARS-UCD1.2/Bos_taurus.ARS-UCD1.2.dna.toplevel.chrom.sizes  sam_reads_in_genes-Colon-pooled -nomulti
python /oak/stanford/groups/akundaje/marinovg/code/transcriptome/SAM_reads_in_genes3_BAM.py /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Bos_taurus-ARS-UCD1.2/Bos_taurus.ARS-UCD1.2.102.gtf Duodenum-pooled-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Bos_taurus-ARS-UCD1.2/Bos_taurus.ARS-UCD1.2.dna.toplevel.chrom.sizes  sam_reads_in_genes-Duodenum-pooled -nomulti
python /oak/stanford/groups/akundaje/marinovg/code/transcriptome/SAM_reads_in_genes3_BAM.py /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Bos_taurus-ARS-UCD1.2/Bos_taurus.ARS-UCD1.2.102.gtf Esophagus-pooled-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Bos_taurus-ARS-UCD1.2/Bos_taurus.ARS-UCD1.2.dna.toplevel.chrom.sizes  sam_reads_in_genes-Esophagus-pooled -nomulti
python /oak/stanford/groups/akundaje/marinovg/code/transcriptome/SAM_reads_in_genes3_BAM.py /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Bos_taurus-ARS-UCD1.2/Bos_taurus.ARS-UCD1.2.102.gtf Heart-pooled-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Bos_taurus-ARS-UCD1.2/Bos_taurus.ARS-UCD1.2.dna.toplevel.chrom.sizes  sam_reads_in_genes-Heart-pooled -nomulti
python /oak/stanford/groups/akundaje/marinovg/code/transcriptome/SAM_reads_in_genes3_BAM.py /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Bos_taurus-ARS-UCD1.2/Bos_taurus.ARS-UCD1.2.102.gtf Hypothalamus-pooled-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Bos_taurus-ARS-UCD1.2/Bos_taurus.ARS-UCD1.2.dna.toplevel.chrom.sizes  sam_reads_in_genes-Hypothalamus-pooled -nomulti
python /oak/stanford/groups/akundaje/marinovg/code/transcriptome/SAM_reads_in_genes3_BAM.py /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Bos_taurus-ARS-UCD1.2/Bos_taurus.ARS-UCD1.2.102.gtf Ileum-pooled-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Bos_taurus-ARS-UCD1.2/Bos_taurus.ARS-UCD1.2.dna.toplevel.chrom.sizes  sam_reads_in_genes-Ileum-pooled -nomulti
python /oak/stanford/groups/akundaje/marinovg/code/transcriptome/SAM_reads_in_genes3_BAM.py /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Bos_taurus-ARS-UCD1.2/Bos_taurus.ARS-UCD1.2.102.gtf Isthmus-pooled-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Bos_taurus-ARS-UCD1.2/Bos_taurus.ARS-UCD1.2.dna.toplevel.chrom.sizes  sam_reads_in_genes-Isthmus-pooled -nomulti
python /oak/stanford/groups/akundaje/marinovg/code/transcriptome/SAM_reads_in_genes3_BAM.py /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Bos_taurus-ARS-UCD1.2/Bos_taurus.ARS-UCD1.2.102.gtf Jejunum-pooled-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Bos_taurus-ARS-UCD1.2/Bos_taurus.ARS-UCD1.2.dna.toplevel.chrom.sizes  sam_reads_in_genes-Jejunum-pooled -nomulti
python /oak/stanford/groups/akundaje/marinovg/code/transcriptome/SAM_reads_in_genes3_BAM.py /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Bos_taurus-ARS-UCD1.2/Bos_taurus.ARS-UCD1.2.102.gtf Kidney-pooled-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Bos_taurus-ARS-UCD1.2/Bos_taurus.ARS-UCD1.2.dna.toplevel.chrom.sizes  sam_reads_in_genes-Kidney-pooled -nomulti
python /oak/stanford/groups/akundaje/marinovg/code/transcriptome/SAM_reads_in_genes3_BAM.py /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Bos_taurus-ARS-UCD1.2/Bos_taurus.ARS-UCD1.2.102.gtf Liver-pooled-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Bos_taurus-ARS-UCD1.2/Bos_taurus.ARS-UCD1.2.dna.toplevel.chrom.sizes  sam_reads_in_genes-Liver-pooled -nomulti
python /oak/stanford/groups/akundaje/marinovg/code/transcriptome/SAM_reads_in_genes3_BAM.py /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Bos_taurus-ARS-UCD1.2/Bos_taurus.ARS-UCD1.2.102.gtf Lung-pooled-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Bos_taurus-ARS-UCD1.2/Bos_taurus.ARS-UCD1.2.dna.toplevel.chrom.sizes  sam_reads_in_genes-Lung-pooled -nomulti
python /oak/stanford/groups/akundaje/marinovg/code/transcriptome/SAM_reads_in_genes3_BAM.py /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Bos_taurus-ARS-UCD1.2/Bos_taurus.ARS-UCD1.2.102.gtf Mammary-pooled-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Bos_taurus-ARS-UCD1.2/Bos_taurus.ARS-UCD1.2.dna.toplevel.chrom.sizes  sam_reads_in_genes-Mammary-pooled -nomulti
python /oak/stanford/groups/akundaje/marinovg/code/transcriptome/SAM_reads_in_genes3_BAM.py /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Bos_taurus-ARS-UCD1.2/Bos_taurus.ARS-UCD1.2.102.gtf Muscle-pooled-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Bos_taurus-ARS-UCD1.2/Bos_taurus.ARS-UCD1.2.dna.toplevel.chrom.sizes  sam_reads_in_genes-Muscle-pooled -nomulti
python /oak/stanford/groups/akundaje/marinovg/code/transcriptome/SAM_reads_in_genes3_BAM.py /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Bos_taurus-ARS-UCD1.2/Bos_taurus.ARS-UCD1.2.102.gtf Omasum-pooled-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Bos_taurus-ARS-UCD1.2/Bos_taurus.ARS-UCD1.2.dna.toplevel.chrom.sizes  sam_reads_in_genes-Omasum-pooled -nomulti
python /oak/stanford/groups/akundaje/marinovg/code/transcriptome/SAM_reads_in_genes3_BAM.py /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Bos_taurus-ARS-UCD1.2/Bos_taurus.ARS-UCD1.2.102.gtf Ovary-pooled-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Bos_taurus-ARS-UCD1.2/Bos_taurus.ARS-UCD1.2.dna.toplevel.chrom.sizes  sam_reads_in_genes-Ovary-pooled -nomulti
python /oak/stanford/groups/akundaje/marinovg/code/transcriptome/SAM_reads_in_genes3_BAM.py /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Bos_taurus-ARS-UCD1.2/Bos_taurus.ARS-UCD1.2.102.gtf Reticulum-pooled-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Bos_taurus-ARS-UCD1.2/Bos_taurus.ARS-UCD1.2.dna.toplevel.chrom.sizes  sam_reads_in_genes-Reticulum-pooled -nomulti
python /oak/stanford/groups/akundaje/marinovg/code/transcriptome/SAM_reads_in_genes3_BAM.py /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Bos_taurus-ARS-UCD1.2/Bos_taurus.ARS-UCD1.2.102.gtf Rumen-pooled-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Bos_taurus-ARS-UCD1.2/Bos_taurus.ARS-UCD1.2.dna.toplevel.chrom.sizes  sam_reads_in_genes-Rumen-pooled -nomulti
python /oak/stanford/groups/akundaje/marinovg/code/transcriptome/SAM_reads_in_genes3_BAM.py /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Bos_taurus-ARS-UCD1.2/Bos_taurus.ARS-UCD1.2.102.gtf Skin-pooled-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Bos_taurus-ARS-UCD1.2/Bos_taurus.ARS-UCD1.2.dna.toplevel.chrom.sizes  sam_reads_in_genes-Skin-pooled -nomulti
python /oak/stanford/groups/akundaje/marinovg/code/transcriptome/SAM_reads_in_genes3_BAM.py /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Bos_taurus-ARS-UCD1.2/Bos_taurus.ARS-UCD1.2.102.gtf Spleen-pooled-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Bos_taurus-ARS-UCD1.2/Bos_taurus.ARS-UCD1.2.dna.toplevel.chrom.sizes  sam_reads_in_genes-Spleen-pooled -nomulti
python /oak/stanford/groups/akundaje/marinovg/code/transcriptome/SAM_reads_in_genes3_BAM.py /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Bos_taurus-ARS-UCD1.2/Bos_taurus.ARS-UCD1.2.102.gtf Testis-pooled-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Bos_taurus-ARS-UCD1.2/Bos_taurus.ARS-UCD1.2.dna.toplevel.chrom.sizes  sam_reads_in_genes-Testis-pooled -nomulti
python /oak/stanford/groups/akundaje/marinovg/code/transcriptome/SAM_reads_in_genes3_BAM.py /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Bos_taurus-ARS-UCD1.2/Bos_taurus.ARS-UCD1.2.102.gtf Thymus-pooled-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Bos_taurus-ARS-UCD1.2/Bos_taurus.ARS-UCD1.2.dna.toplevel.chrom.sizes  sam_reads_in_genes-Thymus-pooled -nomulti
python /oak/stanford/groups/akundaje/marinovg/code/transcriptome/SAM_reads_in_genes3_BAM.py /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Bos_taurus-ARS-UCD1.2/Bos_taurus.ARS-UCD1.2.102.gtf Trachea-pooled-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Bos_taurus-ARS-UCD1.2/Bos_taurus.ARS-UCD1.2.dna.toplevel.chrom.sizes  sam_reads_in_genes-Trachea-pooled -nomulti
python /oak/stanford/groups/akundaje/marinovg/code/transcriptome/SAM_reads_in_genes3_BAM.py /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Bos_taurus-ARS-UCD1.2/Bos_taurus.ARS-UCD1.2.102.gtf UterineEndo-pooled-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Bos_taurus-ARS-UCD1.2/Bos_taurus.ARS-UCD1.2.dna.toplevel.chrom.sizes  sam_reads_in_genes-UterineEndo-pooled -nomulti