python /oak/stanford/groups/akundaje/marinovg/code/makewigglefromBAM-NH.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 Amphioxus_Embryo_15h_CAGE-GSM2837511-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.counts.wig -notitle -end1only
python /oak/stanford/groups/akundaje/marinovg/code/makewigglefromBAM-NH.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 Amphioxus_Embryo_32_Cell_CAGE-GSM2837509-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.counts.wig -notitle -end1only
python /oak/stanford/groups/akundaje/marinovg/code/makewigglefromBAM-NH.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 Amphioxus_Embryo_8h_CAGE-GSM2837510-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.counts.wig -notitle -end1only
python /oak/stanford/groups/akundaje/marinovg/code/makewigglefromBAM-NH.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 Amphioxus_Female_Gonads_CAGE-GSM2837514-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.counts.wig -notitle -end1only
python /oak/stanford/groups/akundaje/marinovg/code/makewigglefromBAM-NH.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 Amphioxus_Hepatic_System_CAGE-GSM2837513-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.counts.wig -notitle -end1only
python /oak/stanford/groups/akundaje/marinovg/code/makewigglefromBAM-NH.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 Amphioxus_Muscle_CAGE-GSM2837515-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.counts.wig -notitle -end1only
python /oak/stanford/groups/akundaje/marinovg/code/makewigglefromBAM-NH.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 Amphioxus_Neural_Tube_CAGE-GSM2837512-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.counts.wig -notitle -end1only
python /oak/stanford/groups/akundaje/marinovg/code/makewigglefromBAM-NH.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 Amphioxus_Embryo_15h_CAGE-GSM2837511-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.RPM.wig -RPM -notitle -end1only
python /oak/stanford/groups/akundaje/marinovg/code/makewigglefromBAM-NH.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 Amphioxus_Embryo_32_Cell_CAGE-GSM2837509-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.RPM.wig -RPM -notitle -end1only
python /oak/stanford/groups/akundaje/marinovg/code/makewigglefromBAM-NH.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 Amphioxus_Embryo_8h_CAGE-GSM2837510-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.RPM.wig -RPM -notitle -end1only
python /oak/stanford/groups/akundaje/marinovg/code/makewigglefromBAM-NH.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 Amphioxus_Female_Gonads_CAGE-GSM2837514-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.RPM.wig -RPM -notitle -end1only
python /oak/stanford/groups/akundaje/marinovg/code/makewigglefromBAM-NH.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 Amphioxus_Hepatic_System_CAGE-GSM2837513-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.RPM.wig -RPM -notitle -end1only
python /oak/stanford/groups/akundaje/marinovg/code/makewigglefromBAM-NH.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 Amphioxus_Muscle_CAGE-GSM2837515-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.RPM.wig -RPM -notitle -end1only
python /oak/stanford/groups/akundaje/marinovg/code/makewigglefromBAM-NH.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 Amphioxus_Neural_Tube_CAGE-GSM2837512-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.RPM.wig -RPM -notitle -end1only
python /oak/stanford/groups/akundaje/marinovg/code/makewigglefromBAM-NH.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 Amphioxus_Embryo_15h_CAGE-GSM2837511-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.unique.RPM.wig -RPM -nomulti -notitle -end1only
python /oak/stanford/groups/akundaje/marinovg/code/makewigglefromBAM-NH.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 Amphioxus_Embryo_32_Cell_CAGE-GSM2837509-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.unique.RPM.wig -RPM -nomulti -notitle -end1only
python /oak/stanford/groups/akundaje/marinovg/code/makewigglefromBAM-NH.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 Amphioxus_Embryo_8h_CAGE-GSM2837510-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.unique.RPM.wig -RPM -nomulti -notitle -end1only
python /oak/stanford/groups/akundaje/marinovg/code/makewigglefromBAM-NH.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 Amphioxus_Female_Gonads_CAGE-GSM2837514-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.unique.RPM.wig -RPM -nomulti -notitle -end1only
python /oak/stanford/groups/akundaje/marinovg/code/makewigglefromBAM-NH.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 Amphioxus_Hepatic_System_CAGE-GSM2837513-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.unique.RPM.wig -RPM -nomulti -notitle -end1only
python /oak/stanford/groups/akundaje/marinovg/code/makewigglefromBAM-NH.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 Amphioxus_Muscle_CAGE-GSM2837515-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.unique.RPM.wig -RPM -nomulti -notitle -end1only
python /oak/stanford/groups/akundaje/marinovg/code/makewigglefromBAM-NH.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 Amphioxus_Neural_Tube_CAGE-GSM2837512-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.unique.RPM.wig -RPM -nomulti -notitle -end1only
python /oak/stanford/groups/akundaje/marinovg/code/makewigglefromBAM-NH.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 Amphioxus_Embryo_15h_CAGE-GSM2837511-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.unique.counts.wig -nomulti -notitle -end1only
python /oak/stanford/groups/akundaje/marinovg/code/makewigglefromBAM-NH.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 Amphioxus_Embryo_32_Cell_CAGE-GSM2837509-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.unique.counts.wig -nomulti -notitle -end1only
python /oak/stanford/groups/akundaje/marinovg/code/makewigglefromBAM-NH.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 Amphioxus_Embryo_8h_CAGE-GSM2837510-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.unique.counts.wig -nomulti -notitle -end1only
python /oak/stanford/groups/akundaje/marinovg/code/makewigglefromBAM-NH.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 Amphioxus_Female_Gonads_CAGE-GSM2837514-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.unique.counts.wig -nomulti -notitle -end1only
python /oak/stanford/groups/akundaje/marinovg/code/makewigglefromBAM-NH.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 Amphioxus_Hepatic_System_CAGE-GSM2837513-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.unique.counts.wig -nomulti -notitle -end1only
python /oak/stanford/groups/akundaje/marinovg/code/makewigglefromBAM-NH.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 Amphioxus_Muscle_CAGE-GSM2837515-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.unique.counts.wig -nomulti -notitle -end1only
python /oak/stanford/groups/akundaje/marinovg/code/makewigglefromBAM-NH.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 Amphioxus_Neural_Tube_CAGE-GSM2837512-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.unique.counts.wig -nomulti -notitle -end1only
python /oak/stanford/groups/akundaje/marinovg/code/makewigglefromBAM-NH.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 Amphioxus_Embryo_15h_CAGE-GSM2837511-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.counts.minus.wig -stranded - -notitle -end1only
python /oak/stanford/groups/akundaje/marinovg/code/makewigglefromBAM-NH.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 Amphioxus_Embryo_32_Cell_CAGE-GSM2837509-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.counts.minus.wig -stranded - -notitle -end1only
python /oak/stanford/groups/akundaje/marinovg/code/makewigglefromBAM-NH.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 Amphioxus_Embryo_8h_CAGE-GSM2837510-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.counts.minus.wig -stranded - -notitle -end1only
python /oak/stanford/groups/akundaje/marinovg/code/makewigglefromBAM-NH.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 Amphioxus_Female_Gonads_CAGE-GSM2837514-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.counts.minus.wig -stranded - -notitle -end1only
python /oak/stanford/groups/akundaje/marinovg/code/makewigglefromBAM-NH.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 Amphioxus_Hepatic_System_CAGE-GSM2837513-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.counts.minus.wig -stranded - -notitle -end1only
python /oak/stanford/groups/akundaje/marinovg/code/makewigglefromBAM-NH.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 Amphioxus_Muscle_CAGE-GSM2837515-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.counts.minus.wig -stranded - -notitle -end1only
python /oak/stanford/groups/akundaje/marinovg/code/makewigglefromBAM-NH.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 Amphioxus_Neural_Tube_CAGE-GSM2837512-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.counts.minus.wig -stranded - -notitle -end1only
python /oak/stanford/groups/akundaje/marinovg/code/makewigglefromBAM-NH.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 Amphioxus_Embryo_15h_CAGE-GSM2837511-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.RPM.minus.wig -stranded - -RPM -notitle -end1only
python /oak/stanford/groups/akundaje/marinovg/code/makewigglefromBAM-NH.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 Amphioxus_Embryo_32_Cell_CAGE-GSM2837509-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.RPM.minus.wig -stranded - -RPM -notitle -end1only
python /oak/stanford/groups/akundaje/marinovg/code/makewigglefromBAM-NH.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 Amphioxus_Embryo_8h_CAGE-GSM2837510-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.RPM.minus.wig -stranded - -RPM -notitle -end1only
python /oak/stanford/groups/akundaje/marinovg/code/makewigglefromBAM-NH.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 Amphioxus_Female_Gonads_CAGE-GSM2837514-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.RPM.minus.wig -stranded - -RPM -notitle -end1only
python /oak/stanford/groups/akundaje/marinovg/code/makewigglefromBAM-NH.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 Amphioxus_Hepatic_System_CAGE-GSM2837513-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.RPM.minus.wig -stranded - -RPM -notitle -end1only
python /oak/stanford/groups/akundaje/marinovg/code/makewigglefromBAM-NH.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 Amphioxus_Muscle_CAGE-GSM2837515-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.RPM.minus.wig -stranded - -RPM -notitle -end1only
python /oak/stanford/groups/akundaje/marinovg/code/makewigglefromBAM-NH.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 Amphioxus_Neural_Tube_CAGE-GSM2837512-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.RPM.minus.wig -stranded - -RPM -notitle -end1only
python /oak/stanford/groups/akundaje/marinovg/code/makewigglefromBAM-NH.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 Amphioxus_Embryo_15h_CAGE-GSM2837511-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.unique.RPM.minus.wig -stranded - -RPM -nomulti -notitle -end1only
python /oak/stanford/groups/akundaje/marinovg/code/makewigglefromBAM-NH.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 Amphioxus_Embryo_32_Cell_CAGE-GSM2837509-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.unique.RPM.minus.wig -stranded - -RPM -nomulti -notitle -end1only
python /oak/stanford/groups/akundaje/marinovg/code/makewigglefromBAM-NH.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 Amphioxus_Embryo_8h_CAGE-GSM2837510-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.unique.RPM.minus.wig -stranded - -RPM -nomulti -notitle -end1only
python /oak/stanford/groups/akundaje/marinovg/code/makewigglefromBAM-NH.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 Amphioxus_Female_Gonads_CAGE-GSM2837514-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.unique.RPM.minus.wig -stranded - -RPM -nomulti -notitle -end1only
python /oak/stanford/groups/akundaje/marinovg/code/makewigglefromBAM-NH.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 Amphioxus_Hepatic_System_CAGE-GSM2837513-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.unique.RPM.minus.wig -stranded - -RPM -nomulti -notitle -end1only
python /oak/stanford/groups/akundaje/marinovg/code/makewigglefromBAM-NH.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 Amphioxus_Muscle_CAGE-GSM2837515-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.unique.RPM.minus.wig -stranded - -RPM -nomulti -notitle -end1only
python /oak/stanford/groups/akundaje/marinovg/code/makewigglefromBAM-NH.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 Amphioxus_Neural_Tube_CAGE-GSM2837512-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.unique.RPM.minus.wig -stranded - -RPM -nomulti -notitle -end1only
python /oak/stanford/groups/akundaje/marinovg/code/makewigglefromBAM-NH.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 Amphioxus_Embryo_15h_CAGE-GSM2837511-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.unique.counts.minus.wig -stranded - -nomulti -notitle -end1only
python /oak/stanford/groups/akundaje/marinovg/code/makewigglefromBAM-NH.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 Amphioxus_Embryo_32_Cell_CAGE-GSM2837509-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.unique.counts.minus.wig -stranded - -nomulti -notitle -end1only
python /oak/stanford/groups/akundaje/marinovg/code/makewigglefromBAM-NH.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 Amphioxus_Embryo_8h_CAGE-GSM2837510-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.unique.counts.minus.wig -stranded - -nomulti -notitle -end1only
python /oak/stanford/groups/akundaje/marinovg/code/makewigglefromBAM-NH.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 Amphioxus_Female_Gonads_CAGE-GSM2837514-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.unique.counts.minus.wig -stranded - -nomulti -notitle -end1only
python /oak/stanford/groups/akundaje/marinovg/code/makewigglefromBAM-NH.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 Amphioxus_Hepatic_System_CAGE-GSM2837513-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.unique.counts.minus.wig -stranded - -nomulti -notitle -end1only
python /oak/stanford/groups/akundaje/marinovg/code/makewigglefromBAM-NH.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 Amphioxus_Muscle_CAGE-GSM2837515-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.unique.counts.minus.wig -stranded - -nomulti -notitle -end1only
python /oak/stanford/groups/akundaje/marinovg/code/makewigglefromBAM-NH.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 Amphioxus_Neural_Tube_CAGE-GSM2837512-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.unique.counts.minus.wig -stranded - -nomulti -notitle -end1only
python /oak/stanford/groups/akundaje/marinovg/code/makewigglefromBAM-NH.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 Amphioxus_Embryo_15h_CAGE-GSM2837511-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.counts.plus.wig -stranded + -notitle -end1only
python /oak/stanford/groups/akundaje/marinovg/code/makewigglefromBAM-NH.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 Amphioxus_Embryo_32_Cell_CAGE-GSM2837509-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.counts.plus.wig -stranded + -notitle -end1only
python /oak/stanford/groups/akundaje/marinovg/code/makewigglefromBAM-NH.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 Amphioxus_Embryo_8h_CAGE-GSM2837510-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.counts.plus.wig -stranded + -notitle -end1only
python /oak/stanford/groups/akundaje/marinovg/code/makewigglefromBAM-NH.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 Amphioxus_Female_Gonads_CAGE-GSM2837514-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.counts.plus.wig -stranded + -notitle -end1only
python /oak/stanford/groups/akundaje/marinovg/code/makewigglefromBAM-NH.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 Amphioxus_Hepatic_System_CAGE-GSM2837513-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.counts.plus.wig -stranded + -notitle -end1only
python /oak/stanford/groups/akundaje/marinovg/code/makewigglefromBAM-NH.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 Amphioxus_Muscle_CAGE-GSM2837515-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.counts.plus.wig -stranded + -notitle -end1only
python /oak/stanford/groups/akundaje/marinovg/code/makewigglefromBAM-NH.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 Amphioxus_Neural_Tube_CAGE-GSM2837512-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.counts.plus.wig -stranded + -notitle -end1only
python /oak/stanford/groups/akundaje/marinovg/code/makewigglefromBAM-NH.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 Amphioxus_Embryo_15h_CAGE-GSM2837511-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.RPM.plus.wig -stranded + -RPM -notitle -end1only
python /oak/stanford/groups/akundaje/marinovg/code/makewigglefromBAM-NH.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 Amphioxus_Embryo_32_Cell_CAGE-GSM2837509-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.RPM.plus.wig -stranded + -RPM -notitle -end1only
python /oak/stanford/groups/akundaje/marinovg/code/makewigglefromBAM-NH.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 Amphioxus_Embryo_8h_CAGE-GSM2837510-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.RPM.plus.wig -stranded + -RPM -notitle -end1only
python /oak/stanford/groups/akundaje/marinovg/code/makewigglefromBAM-NH.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 Amphioxus_Female_Gonads_CAGE-GSM2837514-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.RPM.plus.wig -stranded + -RPM -notitle -end1only
python /oak/stanford/groups/akundaje/marinovg/code/makewigglefromBAM-NH.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 Amphioxus_Hepatic_System_CAGE-GSM2837513-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.RPM.plus.wig -stranded + -RPM -notitle -end1only
python /oak/stanford/groups/akundaje/marinovg/code/makewigglefromBAM-NH.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 Amphioxus_Muscle_CAGE-GSM2837515-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.RPM.plus.wig -stranded + -RPM -notitle -end1only
python /oak/stanford/groups/akundaje/marinovg/code/makewigglefromBAM-NH.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 Amphioxus_Neural_Tube_CAGE-GSM2837512-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.RPM.plus.wig -stranded + -RPM -notitle -end1only
python /oak/stanford/groups/akundaje/marinovg/code/makewigglefromBAM-NH.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 Amphioxus_Embryo_15h_CAGE-GSM2837511-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.unique.RPM.plus.wig -stranded + -RPM -nomulti -notitle -end1only
python /oak/stanford/groups/akundaje/marinovg/code/makewigglefromBAM-NH.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 Amphioxus_Embryo_32_Cell_CAGE-GSM2837509-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.unique.RPM.plus.wig -stranded + -RPM -nomulti -notitle -end1only
python /oak/stanford/groups/akundaje/marinovg/code/makewigglefromBAM-NH.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 Amphioxus_Embryo_8h_CAGE-GSM2837510-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.unique.RPM.plus.wig -stranded + -RPM -nomulti -notitle -end1only
python /oak/stanford/groups/akundaje/marinovg/code/makewigglefromBAM-NH.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 Amphioxus_Female_Gonads_CAGE-GSM2837514-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.unique.RPM.plus.wig -stranded + -RPM -nomulti -notitle -end1only
python /oak/stanford/groups/akundaje/marinovg/code/makewigglefromBAM-NH.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 Amphioxus_Hepatic_System_CAGE-GSM2837513-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.unique.RPM.plus.wig -stranded + -RPM -nomulti -notitle -end1only
python /oak/stanford/groups/akundaje/marinovg/code/makewigglefromBAM-NH.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 Amphioxus_Muscle_CAGE-GSM2837515-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.unique.RPM.plus.wig -stranded + -RPM -nomulti -notitle -end1only
python /oak/stanford/groups/akundaje/marinovg/code/makewigglefromBAM-NH.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 Amphioxus_Neural_Tube_CAGE-GSM2837512-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.unique.RPM.plus.wig -stranded + -RPM -nomulti -notitle -end1only
python /oak/stanford/groups/akundaje/marinovg/code/makewigglefromBAM-NH.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 Amphioxus_Embryo_15h_CAGE-GSM2837511-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.unique.counts.plus.wig -stranded + -nomulti -notitle -end1only
python /oak/stanford/groups/akundaje/marinovg/code/makewigglefromBAM-NH.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 Amphioxus_Embryo_32_Cell_CAGE-GSM2837509-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.unique.counts.plus.wig -stranded + -nomulti -notitle -end1only
python /oak/stanford/groups/akundaje/marinovg/code/makewigglefromBAM-NH.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 Amphioxus_Embryo_8h_CAGE-GSM2837510-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.unique.counts.plus.wig -stranded + -nomulti -notitle -end1only
python /oak/stanford/groups/akundaje/marinovg/code/makewigglefromBAM-NH.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 Amphioxus_Female_Gonads_CAGE-GSM2837514-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.unique.counts.plus.wig -stranded + -nomulti -notitle -end1only
python /oak/stanford/groups/akundaje/marinovg/code/makewigglefromBAM-NH.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 Amphioxus_Hepatic_System_CAGE-GSM2837513-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.unique.counts.plus.wig -stranded + -nomulti -notitle -end1only
python /oak/stanford/groups/akundaje/marinovg/code/makewigglefromBAM-NH.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 Amphioxus_Muscle_CAGE-GSM2837515-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.unique.counts.plus.wig -stranded + -nomulti -notitle -end1only
python /oak/stanford/groups/akundaje/marinovg/code/makewigglefromBAM-NH.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 Amphioxus_Neural_Tube_CAGE-GSM2837512-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.unique.counts.plus.wig -stranded + -nomulti -notitle -end1only
python /oak/stanford/groups/akundaje/marinovg/code/make5primeWigglefromBAM-NH.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 Amphioxus_Embryo_15h_CAGE-GSM2837511-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.counts.5p.wig -notitle -end1only
python /oak/stanford/groups/akundaje/marinovg/code/make5primeWigglefromBAM-NH.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 Amphioxus_Embryo_32_Cell_CAGE-GSM2837509-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.counts.5p.wig -notitle -end1only
python /oak/stanford/groups/akundaje/marinovg/code/make5primeWigglefromBAM-NH.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 Amphioxus_Embryo_8h_CAGE-GSM2837510-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.counts.5p.wig -notitle -end1only
python /oak/stanford/groups/akundaje/marinovg/code/make5primeWigglefromBAM-NH.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 Amphioxus_Female_Gonads_CAGE-GSM2837514-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.counts.5p.wig -notitle -end1only
python /oak/stanford/groups/akundaje/marinovg/code/make5primeWigglefromBAM-NH.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 Amphioxus_Hepatic_System_CAGE-GSM2837513-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.counts.5p.wig -notitle -end1only
python /oak/stanford/groups/akundaje/marinovg/code/make5primeWigglefromBAM-NH.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 Amphioxus_Muscle_CAGE-GSM2837515-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.counts.5p.wig -notitle -end1only
python /oak/stanford/groups/akundaje/marinovg/code/make5primeWigglefromBAM-NH.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 Amphioxus_Neural_Tube_CAGE-GSM2837512-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.counts.5p.wig -notitle -end1only
python /oak/stanford/groups/akundaje/marinovg/code/make5primeWigglefromBAM-NH.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 Amphioxus_Embryo_15h_CAGE-GSM2837511-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.RPM.5p.wig -RPM -notitle -end1only
python /oak/stanford/groups/akundaje/marinovg/code/make5primeWigglefromBAM-NH.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 Amphioxus_Embryo_32_Cell_CAGE-GSM2837509-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.RPM.5p.wig -RPM -notitle -end1only
python /oak/stanford/groups/akundaje/marinovg/code/make5primeWigglefromBAM-NH.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 Amphioxus_Embryo_8h_CAGE-GSM2837510-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.RPM.5p.wig -RPM -notitle -end1only
python /oak/stanford/groups/akundaje/marinovg/code/make5primeWigglefromBAM-NH.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 Amphioxus_Female_Gonads_CAGE-GSM2837514-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.RPM.5p.wig -RPM -notitle -end1only
python /oak/stanford/groups/akundaje/marinovg/code/make5primeWigglefromBAM-NH.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 Amphioxus_Hepatic_System_CAGE-GSM2837513-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.RPM.5p.wig -RPM -notitle -end1only
python /oak/stanford/groups/akundaje/marinovg/code/make5primeWigglefromBAM-NH.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 Amphioxus_Muscle_CAGE-GSM2837515-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.RPM.5p.wig -RPM -notitle -end1only
python /oak/stanford/groups/akundaje/marinovg/code/make5primeWigglefromBAM-NH.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 Amphioxus_Neural_Tube_CAGE-GSM2837512-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.RPM.5p.wig -RPM -notitle -end1only
python /oak/stanford/groups/akundaje/marinovg/code/make5primeWigglefromBAM-NH.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 Amphioxus_Embryo_15h_CAGE-GSM2837511-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.unique.RPM.5p.wig -RPM -nomulti -notitle -end1only
python /oak/stanford/groups/akundaje/marinovg/code/make5primeWigglefromBAM-NH.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 Amphioxus_Embryo_32_Cell_CAGE-GSM2837509-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.unique.RPM.5p.wig -RPM -nomulti -notitle -end1only
python /oak/stanford/groups/akundaje/marinovg/code/make5primeWigglefromBAM-NH.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 Amphioxus_Embryo_8h_CAGE-GSM2837510-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.unique.RPM.5p.wig -RPM -nomulti -notitle -end1only
python /oak/stanford/groups/akundaje/marinovg/code/make5primeWigglefromBAM-NH.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 Amphioxus_Female_Gonads_CAGE-GSM2837514-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.unique.RPM.5p.wig -RPM -nomulti -notitle -end1only
python /oak/stanford/groups/akundaje/marinovg/code/make5primeWigglefromBAM-NH.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 Amphioxus_Hepatic_System_CAGE-GSM2837513-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.unique.RPM.5p.wig -RPM -nomulti -notitle -end1only
python /oak/stanford/groups/akundaje/marinovg/code/make5primeWigglefromBAM-NH.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 Amphioxus_Muscle_CAGE-GSM2837515-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.unique.RPM.5p.wig -RPM -nomulti -notitle -end1only
python /oak/stanford/groups/akundaje/marinovg/code/make5primeWigglefromBAM-NH.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 Amphioxus_Neural_Tube_CAGE-GSM2837512-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.unique.RPM.5p.wig -RPM -nomulti -notitle -end1only
python /oak/stanford/groups/akundaje/marinovg/code/make5primeWigglefromBAM-NH.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 Amphioxus_Embryo_15h_CAGE-GSM2837511-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.unique.counts.5p.wig -nomulti -notitle -end1only
python /oak/stanford/groups/akundaje/marinovg/code/make5primeWigglefromBAM-NH.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 Amphioxus_Embryo_32_Cell_CAGE-GSM2837509-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.unique.counts.5p.wig -nomulti -notitle -end1only
python /oak/stanford/groups/akundaje/marinovg/code/make5primeWigglefromBAM-NH.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 Amphioxus_Embryo_8h_CAGE-GSM2837510-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.unique.counts.5p.wig -nomulti -notitle -end1only
python /oak/stanford/groups/akundaje/marinovg/code/make5primeWigglefromBAM-NH.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 Amphioxus_Female_Gonads_CAGE-GSM2837514-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.unique.counts.5p.wig -nomulti -notitle -end1only
python /oak/stanford/groups/akundaje/marinovg/code/make5primeWigglefromBAM-NH.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 Amphioxus_Hepatic_System_CAGE-GSM2837513-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.unique.counts.5p.wig -nomulti -notitle -end1only
python /oak/stanford/groups/akundaje/marinovg/code/make5primeWigglefromBAM-NH.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 Amphioxus_Muscle_CAGE-GSM2837515-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.unique.counts.5p.wig -nomulti -notitle -end1only
python /oak/stanford/groups/akundaje/marinovg/code/make5primeWigglefromBAM-NH.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 Amphioxus_Neural_Tube_CAGE-GSM2837512-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.unique.counts.5p.wig -nomulti -notitle -end1only
python /oak/stanford/groups/akundaje/marinovg/code/make5primeWigglefromBAM-NH.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 Amphioxus_Embryo_15h_CAGE-GSM2837511-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.counts.minus.5p.wig -stranded - -notitle -end1only
python /oak/stanford/groups/akundaje/marinovg/code/make5primeWigglefromBAM-NH.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 Amphioxus_Embryo_32_Cell_CAGE-GSM2837509-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.counts.minus.5p.wig -stranded - -notitle -end1only
python /oak/stanford/groups/akundaje/marinovg/code/make5primeWigglefromBAM-NH.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 Amphioxus_Embryo_8h_CAGE-GSM2837510-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.counts.minus.5p.wig -stranded - -notitle -end1only
python /oak/stanford/groups/akundaje/marinovg/code/make5primeWigglefromBAM-NH.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 Amphioxus_Female_Gonads_CAGE-GSM2837514-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.counts.minus.5p.wig -stranded - -notitle -end1only
python /oak/stanford/groups/akundaje/marinovg/code/make5primeWigglefromBAM-NH.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 Amphioxus_Hepatic_System_CAGE-GSM2837513-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.counts.minus.5p.wig -stranded - -notitle -end1only
python /oak/stanford/groups/akundaje/marinovg/code/make5primeWigglefromBAM-NH.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 Amphioxus_Muscle_CAGE-GSM2837515-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.counts.minus.5p.wig -stranded - -notitle -end1only
python /oak/stanford/groups/akundaje/marinovg/code/make5primeWigglefromBAM-NH.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 Amphioxus_Neural_Tube_CAGE-GSM2837512-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.counts.minus.5p.wig -stranded - -notitle -end1only
python /oak/stanford/groups/akundaje/marinovg/code/make5primeWigglefromBAM-NH.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 Amphioxus_Embryo_15h_CAGE-GSM2837511-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.RPM.minus.5p.wig -stranded - -RPM -notitle -end1only
python /oak/stanford/groups/akundaje/marinovg/code/make5primeWigglefromBAM-NH.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 Amphioxus_Embryo_32_Cell_CAGE-GSM2837509-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.RPM.minus.5p.wig -stranded - -RPM -notitle -end1only
python /oak/stanford/groups/akundaje/marinovg/code/make5primeWigglefromBAM-NH.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 Amphioxus_Embryo_8h_CAGE-GSM2837510-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.RPM.minus.5p.wig -stranded - -RPM -notitle -end1only
python /oak/stanford/groups/akundaje/marinovg/code/make5primeWigglefromBAM-NH.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 Amphioxus_Female_Gonads_CAGE-GSM2837514-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.RPM.minus.5p.wig -stranded - -RPM -notitle -end1only
python /oak/stanford/groups/akundaje/marinovg/code/make5primeWigglefromBAM-NH.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 Amphioxus_Hepatic_System_CAGE-GSM2837513-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.RPM.minus.5p.wig -stranded - -RPM -notitle -end1only
python /oak/stanford/groups/akundaje/marinovg/code/make5primeWigglefromBAM-NH.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 Amphioxus_Muscle_CAGE-GSM2837515-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.RPM.minus.5p.wig -stranded - -RPM -notitle -end1only
python /oak/stanford/groups/akundaje/marinovg/code/make5primeWigglefromBAM-NH.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 Amphioxus_Neural_Tube_CAGE-GSM2837512-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.RPM.minus.5p.wig -stranded - -RPM -notitle -end1only
python /oak/stanford/groups/akundaje/marinovg/code/make5primeWigglefromBAM-NH.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 Amphioxus_Embryo_15h_CAGE-GSM2837511-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.unique.RPM.minus.5p.wig -stranded - -RPM -nomulti -notitle -end1only
python /oak/stanford/groups/akundaje/marinovg/code/make5primeWigglefromBAM-NH.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 Amphioxus_Embryo_32_Cell_CAGE-GSM2837509-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.unique.RPM.minus.5p.wig -stranded - -RPM -nomulti -notitle -end1only
python /oak/stanford/groups/akundaje/marinovg/code/make5primeWigglefromBAM-NH.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 Amphioxus_Embryo_8h_CAGE-GSM2837510-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.unique.RPM.minus.5p.wig -stranded - -RPM -nomulti -notitle -end1only
python /oak/stanford/groups/akundaje/marinovg/code/make5primeWigglefromBAM-NH.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 Amphioxus_Female_Gonads_CAGE-GSM2837514-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.unique.RPM.minus.5p.wig -stranded - -RPM -nomulti -notitle -end1only
python /oak/stanford/groups/akundaje/marinovg/code/make5primeWigglefromBAM-NH.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 Amphioxus_Hepatic_System_CAGE-GSM2837513-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.unique.RPM.minus.5p.wig -stranded - -RPM -nomulti -notitle -end1only
python /oak/stanford/groups/akundaje/marinovg/code/make5primeWigglefromBAM-NH.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 Amphioxus_Muscle_CAGE-GSM2837515-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.unique.RPM.minus.5p.wig -stranded - -RPM -nomulti -notitle -end1only
python /oak/stanford/groups/akundaje/marinovg/code/make5primeWigglefromBAM-NH.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 Amphioxus_Neural_Tube_CAGE-GSM2837512-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.unique.RPM.minus.5p.wig -stranded - -RPM -nomulti -notitle -end1only
python /oak/stanford/groups/akundaje/marinovg/code/make5primeWigglefromBAM-NH.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 Amphioxus_Embryo_15h_CAGE-GSM2837511-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.unique.counts.minus.5p.wig -stranded - -nomulti -notitle -end1only
python /oak/stanford/groups/akundaje/marinovg/code/make5primeWigglefromBAM-NH.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 Amphioxus_Embryo_32_Cell_CAGE-GSM2837509-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.unique.counts.minus.5p.wig -stranded - -nomulti -notitle -end1only
python /oak/stanford/groups/akundaje/marinovg/code/make5primeWigglefromBAM-NH.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 Amphioxus_Embryo_8h_CAGE-GSM2837510-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.unique.counts.minus.5p.wig -stranded - -nomulti -notitle -end1only
python /oak/stanford/groups/akundaje/marinovg/code/make5primeWigglefromBAM-NH.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 Amphioxus_Female_Gonads_CAGE-GSM2837514-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.unique.counts.minus.5p.wig -stranded - -nomulti -notitle -end1only
python /oak/stanford/groups/akundaje/marinovg/code/make5primeWigglefromBAM-NH.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 Amphioxus_Hepatic_System_CAGE-GSM2837513-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.unique.counts.minus.5p.wig -stranded - -nomulti -notitle -end1only
python /oak/stanford/groups/akundaje/marinovg/code/make5primeWigglefromBAM-NH.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 Amphioxus_Muscle_CAGE-GSM2837515-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.unique.counts.minus.5p.wig -stranded - -nomulti -notitle -end1only
python /oak/stanford/groups/akundaje/marinovg/code/make5primeWigglefromBAM-NH.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 Amphioxus_Neural_Tube_CAGE-GSM2837512-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.unique.counts.minus.5p.wig -stranded - -nomulti -notitle -end1only
python /oak/stanford/groups/akundaje/marinovg/code/make5primeWigglefromBAM-NH.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 Amphioxus_Embryo_15h_CAGE-GSM2837511-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.counts.plus.5p.wig -stranded + -notitle -end1only
python /oak/stanford/groups/akundaje/marinovg/code/make5primeWigglefromBAM-NH.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 Amphioxus_Embryo_32_Cell_CAGE-GSM2837509-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.counts.plus.5p.wig -stranded + -notitle -end1only
python /oak/stanford/groups/akundaje/marinovg/code/make5primeWigglefromBAM-NH.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 Amphioxus_Embryo_8h_CAGE-GSM2837510-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.counts.plus.5p.wig -stranded + -notitle -end1only
python /oak/stanford/groups/akundaje/marinovg/code/make5primeWigglefromBAM-NH.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 Amphioxus_Female_Gonads_CAGE-GSM2837514-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.counts.plus.5p.wig -stranded + -notitle -end1only
python /oak/stanford/groups/akundaje/marinovg/code/make5primeWigglefromBAM-NH.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 Amphioxus_Hepatic_System_CAGE-GSM2837513-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.counts.plus.5p.wig -stranded + -notitle -end1only
python /oak/stanford/groups/akundaje/marinovg/code/make5primeWigglefromBAM-NH.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 Amphioxus_Muscle_CAGE-GSM2837515-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.counts.plus.5p.wig -stranded + -notitle -end1only
python /oak/stanford/groups/akundaje/marinovg/code/make5primeWigglefromBAM-NH.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 Amphioxus_Neural_Tube_CAGE-GSM2837512-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.counts.plus.5p.wig -stranded + -notitle -end1only
python /oak/stanford/groups/akundaje/marinovg/code/make5primeWigglefromBAM-NH.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 Amphioxus_Embryo_15h_CAGE-GSM2837511-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.RPM.plus.5p.wig -stranded + -RPM -notitle -end1only
python /oak/stanford/groups/akundaje/marinovg/code/make5primeWigglefromBAM-NH.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 Amphioxus_Embryo_32_Cell_CAGE-GSM2837509-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.RPM.plus.5p.wig -stranded + -RPM -notitle -end1only
python /oak/stanford/groups/akundaje/marinovg/code/make5primeWigglefromBAM-NH.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 Amphioxus_Embryo_8h_CAGE-GSM2837510-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.RPM.plus.5p.wig -stranded + -RPM -notitle -end1only
python /oak/stanford/groups/akundaje/marinovg/code/make5primeWigglefromBAM-NH.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 Amphioxus_Female_Gonads_CAGE-GSM2837514-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.RPM.plus.5p.wig -stranded + -RPM -notitle -end1only
python /oak/stanford/groups/akundaje/marinovg/code/make5primeWigglefromBAM-NH.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 Amphioxus_Hepatic_System_CAGE-GSM2837513-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.RPM.plus.5p.wig -stranded + -RPM -notitle -end1only
python /oak/stanford/groups/akundaje/marinovg/code/make5primeWigglefromBAM-NH.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 Amphioxus_Muscle_CAGE-GSM2837515-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.RPM.plus.5p.wig -stranded + -RPM -notitle -end1only
python /oak/stanford/groups/akundaje/marinovg/code/make5primeWigglefromBAM-NH.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 Amphioxus_Neural_Tube_CAGE-GSM2837512-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.RPM.plus.5p.wig -stranded + -RPM -notitle -end1only
python /oak/stanford/groups/akundaje/marinovg/code/make5primeWigglefromBAM-NH.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 Amphioxus_Embryo_15h_CAGE-GSM2837511-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.unique.RPM.plus.5p.wig -stranded + -RPM -nomulti -notitle -end1only
python /oak/stanford/groups/akundaje/marinovg/code/make5primeWigglefromBAM-NH.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 Amphioxus_Embryo_32_Cell_CAGE-GSM2837509-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.unique.RPM.plus.5p.wig -stranded + -RPM -nomulti -notitle -end1only
python /oak/stanford/groups/akundaje/marinovg/code/make5primeWigglefromBAM-NH.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 Amphioxus_Embryo_8h_CAGE-GSM2837510-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.unique.RPM.plus.5p.wig -stranded + -RPM -nomulti -notitle -end1only
python /oak/stanford/groups/akundaje/marinovg/code/make5primeWigglefromBAM-NH.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 Amphioxus_Female_Gonads_CAGE-GSM2837514-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.unique.RPM.plus.5p.wig -stranded + -RPM -nomulti -notitle -end1only
python /oak/stanford/groups/akundaje/marinovg/code/make5primeWigglefromBAM-NH.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 Amphioxus_Hepatic_System_CAGE-GSM2837513-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.unique.RPM.plus.5p.wig -stranded + -RPM -nomulti -notitle -end1only
python /oak/stanford/groups/akundaje/marinovg/code/make5primeWigglefromBAM-NH.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 Amphioxus_Muscle_CAGE-GSM2837515-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.unique.RPM.plus.5p.wig -stranded + -RPM -nomulti -notitle -end1only
python /oak/stanford/groups/akundaje/marinovg/code/make5primeWigglefromBAM-NH.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 Amphioxus_Neural_Tube_CAGE-GSM2837512-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.unique.RPM.plus.5p.wig -stranded + -RPM -nomulti -notitle -end1only
python /oak/stanford/groups/akundaje/marinovg/code/make5primeWigglefromBAM-NH.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 Amphioxus_Embryo_15h_CAGE-GSM2837511-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.unique.counts.plus.5p.wig -stranded + -nomulti -notitle -end1only
python /oak/stanford/groups/akundaje/marinovg/code/make5primeWigglefromBAM-NH.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 Amphioxus_Embryo_32_Cell_CAGE-GSM2837509-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.unique.counts.plus.5p.wig -stranded + -nomulti -notitle -end1only
python /oak/stanford/groups/akundaje/marinovg/code/make5primeWigglefromBAM-NH.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 Amphioxus_Embryo_8h_CAGE-GSM2837510-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.unique.counts.plus.5p.wig -stranded + -nomulti -notitle -end1only
python /oak/stanford/groups/akundaje/marinovg/code/make5primeWigglefromBAM-NH.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 Amphioxus_Female_Gonads_CAGE-GSM2837514-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.unique.counts.plus.5p.wig -stranded + -nomulti -notitle -end1only
python /oak/stanford/groups/akundaje/marinovg/code/make5primeWigglefromBAM-NH.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 Amphioxus_Hepatic_System_CAGE-GSM2837513-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.unique.counts.plus.5p.wig -stranded + -nomulti -notitle -end1only
python /oak/stanford/groups/akundaje/marinovg/code/make5primeWigglefromBAM-NH.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 Amphioxus_Muscle_CAGE-GSM2837515-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.unique.counts.plus.5p.wig -stranded + -nomulti -notitle -end1only
python /oak/stanford/groups/akundaje/marinovg/code/make5primeWigglefromBAM-NH.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 Amphioxus_Neural_Tube_CAGE-GSM2837512-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.unique.counts.plus.5p.wig -stranded + -nomulti -notitle -end1only