python /oak/stanford/groups/akundaje/marinovg/code/transcriptome/RAMPAGE-clusters-V2.py Adipose-pooled-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.102.gtf 200 200 100 Adipose-pooled-STAR-2.5.3a.RAMPAGE-clusters-V2.bed
python /oak/stanford/groups/akundaje/marinovg/code/transcriptome/RAMPAGE-clusters-V2.py Bladder-pooled-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.102.gtf 200 200 100 Bladder-pooled-STAR-2.5.3a.RAMPAGE-clusters-V2.bed
python /oak/stanford/groups/akundaje/marinovg/code/transcriptome/RAMPAGE-clusters-V2.py BoneMarrow-pooled-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.102.gtf 200 200 100 BoneMarrow-pooled-STAR-2.5.3a.RAMPAGE-clusters-V2.bed
python /oak/stanford/groups/akundaje/marinovg/code/transcriptome/RAMPAGE-clusters-V2.py BrainCortex-pooled-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.102.gtf 200 200 100 BrainCortex-pooled-STAR-2.5.3a.RAMPAGE-clusters-V2.bed
python /oak/stanford/groups/akundaje/marinovg/code/transcriptome/RAMPAGE-clusters-V2.py Cerebellum-pooled-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.102.gtf 200 200 100 Cerebellum-pooled-STAR-2.5.3a.RAMPAGE-clusters-V2.bed
python /oak/stanford/groups/akundaje/marinovg/code/transcriptome/RAMPAGE-clusters-V2.py Colon-pooled-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.102.gtf 200 200 100 Colon-pooled-STAR-2.5.3a.RAMPAGE-clusters-V2.bed
python /oak/stanford/groups/akundaje/marinovg/code/transcriptome/RAMPAGE-clusters-V2.py Duodenum-pooled-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.102.gtf 200 200 100 Duodenum-pooled-STAR-2.5.3a.RAMPAGE-clusters-V2.bed
python /oak/stanford/groups/akundaje/marinovg/code/transcriptome/RAMPAGE-clusters-V2.py Esophagus-pooled-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.102.gtf 200 200 100 Esophagus-pooled-STAR-2.5.3a.RAMPAGE-clusters-V2.bed
python /oak/stanford/groups/akundaje/marinovg/code/transcriptome/RAMPAGE-clusters-V2.py Heart-pooled-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.102.gtf 200 200 100 Heart-pooled-STAR-2.5.3a.RAMPAGE-clusters-V2.bed
python /oak/stanford/groups/akundaje/marinovg/code/transcriptome/RAMPAGE-clusters-V2.py Hypothalamus-pooled-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.102.gtf 200 200 100 Hypothalamus-pooled-STAR-2.5.3a.RAMPAGE-clusters-V2.bed
python /oak/stanford/groups/akundaje/marinovg/code/transcriptome/RAMPAGE-clusters-V2.py Ileum-pooled-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.102.gtf 200 200 100 Ileum-pooled-STAR-2.5.3a.RAMPAGE-clusters-V2.bed
python /oak/stanford/groups/akundaje/marinovg/code/transcriptome/RAMPAGE-clusters-V2.py Jejunum-pooled-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.102.gtf 200 200 100 Jejunum-pooled-STAR-2.5.3a.RAMPAGE-clusters-V2.bed
python /oak/stanford/groups/akundaje/marinovg/code/transcriptome/RAMPAGE-clusters-V2.py Kidney-pooled-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.102.gtf 200 200 100 Kidney-pooled-STAR-2.5.3a.RAMPAGE-clusters-V2.bed
python /oak/stanford/groups/akundaje/marinovg/code/transcriptome/RAMPAGE-clusters-V2.py Liver-pooled-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.102.gtf 200 200 100 Liver-pooled-STAR-2.5.3a.RAMPAGE-clusters-V2.bed
python /oak/stanford/groups/akundaje/marinovg/code/transcriptome/RAMPAGE-clusters-V2.py Lung-pooled-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.102.gtf 200 200 100 Lung-pooled-STAR-2.5.3a.RAMPAGE-clusters-V2.bed
python /oak/stanford/groups/akundaje/marinovg/code/transcriptome/RAMPAGE-clusters-V2.py Lymphoid-pooled-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.102.gtf 200 200 100 Lymphoid-pooled-STAR-2.5.3a.RAMPAGE-clusters-V2.bed
python /oak/stanford/groups/akundaje/marinovg/code/transcriptome/RAMPAGE-clusters-V2.py Muscle-pooled-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.102.gtf 200 200 100 Muscle-pooled-STAR-2.5.3a.RAMPAGE-clusters-V2.bed
python /oak/stanford/groups/akundaje/marinovg/code/transcriptome/RAMPAGE-clusters-V2.py Skin-pooled-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.102.gtf 200 200 100 Skin-pooled-STAR-2.5.3a.RAMPAGE-clusters-V2.bed
python /oak/stanford/groups/akundaje/marinovg/code/transcriptome/RAMPAGE-clusters-V2.py Spleen-pooled-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.102.gtf 200 200 100 Spleen-pooled-STAR-2.5.3a.RAMPAGE-clusters-V2.bed
python /oak/stanford/groups/akundaje/marinovg/code/transcriptome/RAMPAGE-clusters-V2.py Thymus-pooled-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.102.gtf 200 200 100 Thymus-pooled-STAR-2.5.3a.RAMPAGE-clusters-V2.bed
python /oak/stanford/groups/akundaje/marinovg/code/transcriptome/RAMPAGE-clusters-V2.py Thyroid-pooled-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.102.gtf 200 200 100 Thyroid-pooled-STAR-2.5.3a.RAMPAGE-clusters-V2.bed
python /oak/stanford/groups/akundaje/marinovg/code/transcriptome/RAMPAGE-clusters-V2.py Trachea-pooled-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.dna.toplevel.chrom.sizes /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/Sus_scrofa.Sscrofa11.1.102.gtf 200 200 100 Trachea-pooled-STAR-2.5.3a.RAMPAGE-clusters-V2.bed