python /oak/stanford/groups/akundaje/marinovg/code/transcriptome/RAMPAGE-clusters-V2.py Amphioxus_Embryo_15h_CAGE-GSM2837511-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Cephalochordata/Branchiostoma_lanceolatum-Bl71nemr/GCA_900088365.1_Bl71nemr_genomic.chrom.sizes zz 200 200 100 Amphioxus_Embryo_15h_CAGE-GSM2837511-STAR-2.5.3a.RAMPAGE-clusters-V2.bed
python /oak/stanford/groups/akundaje/marinovg/code/transcriptome/RAMPAGE-clusters-V2.py Amphioxus_Embryo_32_Cell_CAGE-GSM2837509-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Cephalochordata/Branchiostoma_lanceolatum-Bl71nemr/GCA_900088365.1_Bl71nemr_genomic.chrom.sizes zz 200 200 100 Amphioxus_Embryo_32_Cell_CAGE-GSM2837509-STAR-2.5.3a.RAMPAGE-clusters-V2.bed
python /oak/stanford/groups/akundaje/marinovg/code/transcriptome/RAMPAGE-clusters-V2.py Amphioxus_Embryo_8h_CAGE-GSM2837510-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Cephalochordata/Branchiostoma_lanceolatum-Bl71nemr/GCA_900088365.1_Bl71nemr_genomic.chrom.sizes zz 200 200 100 Amphioxus_Embryo_8h_CAGE-GSM2837510-STAR-2.5.3a.RAMPAGE-clusters-V2.bed
python /oak/stanford/groups/akundaje/marinovg/code/transcriptome/RAMPAGE-clusters-V2.py Amphioxus_Female_Gonads_CAGE-GSM2837514-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Cephalochordata/Branchiostoma_lanceolatum-Bl71nemr/GCA_900088365.1_Bl71nemr_genomic.chrom.sizes zz 200 200 100 Amphioxus_Female_Gonads_CAGE-GSM2837514-STAR-2.5.3a.RAMPAGE-clusters-V2.bed
python /oak/stanford/groups/akundaje/marinovg/code/transcriptome/RAMPAGE-clusters-V2.py Amphioxus_Hepatic_System_CAGE-GSM2837513-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Cephalochordata/Branchiostoma_lanceolatum-Bl71nemr/GCA_900088365.1_Bl71nemr_genomic.chrom.sizes zz 200 200 100 Amphioxus_Hepatic_System_CAGE-GSM2837513-STAR-2.5.3a.RAMPAGE-clusters-V2.bed
python /oak/stanford/groups/akundaje/marinovg/code/transcriptome/RAMPAGE-clusters-V2.py Amphioxus_Muscle_CAGE-GSM2837515-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Cephalochordata/Branchiostoma_lanceolatum-Bl71nemr/GCA_900088365.1_Bl71nemr_genomic.chrom.sizes zz 200 200 100 Amphioxus_Muscle_CAGE-GSM2837515-STAR-2.5.3a.RAMPAGE-clusters-V2.bed
python /oak/stanford/groups/akundaje/marinovg/code/transcriptome/RAMPAGE-clusters-V2.py Amphioxus_Neural_Tube_CAGE-GSM2837512-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Cephalochordata/Branchiostoma_lanceolatum-Bl71nemr/GCA_900088365.1_Bl71nemr_genomic.chrom.sizes zz 200 200 100 Amphioxus_Neural_Tube_CAGE-GSM2837512-STAR-2.5.3a.RAMPAGE-clusters-V2.bed