python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py Adipose-pooled-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam  SAMstats-Adipose-pooled -bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Birds/Gallus_gallus-GRCg6a/Gallus_gallus.GRCg6a.dna.toplevel.chrom.sizes  samtools -paired 
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py BoneMarrow-pooled-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam  SAMstats-BoneMarrow-pooled -bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Birds/Gallus_gallus-GRCg6a/Gallus_gallus.GRCg6a.dna.toplevel.chrom.sizes  samtools -paired 
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py BrainCortex-pooled-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam  SAMstats-BrainCortex-pooled -bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Birds/Gallus_gallus-GRCg6a/Gallus_gallus.GRCg6a.dna.toplevel.chrom.sizes  samtools -paired 
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py Cecum-pooled-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam  SAMstats-Cecum-pooled -bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Birds/Gallus_gallus-GRCg6a/Gallus_gallus.GRCg6a.dna.toplevel.chrom.sizes  samtools -paired 
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py Cerebellum-pooled-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam  SAMstats-Cerebellum-pooled -bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Birds/Gallus_gallus-GRCg6a/Gallus_gallus.GRCg6a.dna.toplevel.chrom.sizes  samtools -paired 
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py Colon-pooled-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam  SAMstats-Colon-pooled -bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Birds/Gallus_gallus-GRCg6a/Gallus_gallus.GRCg6a.dna.toplevel.chrom.sizes  samtools -paired 
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py Duodenum-pooled-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam  SAMstats-Duodenum-pooled -bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Birds/Gallus_gallus-GRCg6a/Gallus_gallus.GRCg6a.dna.toplevel.chrom.sizes  samtools -paired 
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py Esophagus-pooled-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam  SAMstats-Esophagus-pooled -bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Birds/Gallus_gallus-GRCg6a/Gallus_gallus.GRCg6a.dna.toplevel.chrom.sizes  samtools -paired 
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py Gizzard-pooled-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam  SAMstats-Gizzard-pooled -bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Birds/Gallus_gallus-GRCg6a/Gallus_gallus.GRCg6a.dna.toplevel.chrom.sizes  samtools -paired 
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py Heart-pooled-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam  SAMstats-Heart-pooled -bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Birds/Gallus_gallus-GRCg6a/Gallus_gallus.GRCg6a.dna.toplevel.chrom.sizes  samtools -paired 
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py Hypothalamus-pooled-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam  SAMstats-Hypothalamus-pooled -bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Birds/Gallus_gallus-GRCg6a/Gallus_gallus.GRCg6a.dna.toplevel.chrom.sizes  samtools -paired 
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py Ileum-pooled-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam  SAMstats-Ileum-pooled -bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Birds/Gallus_gallus-GRCg6a/Gallus_gallus.GRCg6a.dna.toplevel.chrom.sizes  samtools -paired 
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py Jejunum-pooled-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam  SAMstats-Jejunum-pooled -bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Birds/Gallus_gallus-GRCg6a/Gallus_gallus.GRCg6a.dna.toplevel.chrom.sizes  samtools -paired 
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py Kidney-pooled-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam  SAMstats-Kidney-pooled -bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Birds/Gallus_gallus-GRCg6a/Gallus_gallus.GRCg6a.dna.toplevel.chrom.sizes  samtools -paired 
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py Liver-pooled-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam  SAMstats-Liver-pooled -bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Birds/Gallus_gallus-GRCg6a/Gallus_gallus.GRCg6a.dna.toplevel.chrom.sizes  samtools -paired 
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py Lung-pooled-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam  SAMstats-Lung-pooled -bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Birds/Gallus_gallus-GRCg6a/Gallus_gallus.GRCg6a.dna.toplevel.chrom.sizes  samtools -paired 
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py Ovary-pooled-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam  SAMstats-Ovary-pooled -bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Birds/Gallus_gallus-GRCg6a/Gallus_gallus.GRCg6a.dna.toplevel.chrom.sizes  samtools -paired 
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py Spleen-pooled-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam  SAMstats-Spleen-pooled -bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Birds/Gallus_gallus-GRCg6a/Gallus_gallus.GRCg6a.dna.toplevel.chrom.sizes  samtools -paired 
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py Testis-pooled-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam  SAMstats-Testis-pooled -bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Birds/Gallus_gallus-GRCg6a/Gallus_gallus.GRCg6a.dna.toplevel.chrom.sizes  samtools -paired 
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py Thymus-pooled-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam  SAMstats-Thymus-pooled -bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Birds/Gallus_gallus-GRCg6a/Gallus_gallus.GRCg6a.dna.toplevel.chrom.sizes  samtools -paired 
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py Trachea-pooled-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam  SAMstats-Trachea-pooled -bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Birds/Gallus_gallus-GRCg6a/Gallus_gallus.GRCg6a.dna.toplevel.chrom.sizes  samtools -paired