python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py RAMPAGE_in_B73_coleoptilar_node-pooled-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam SAMstats-RAMPAGE_in_B73_coleoptilar_node-pooled -bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Zea_mays-Zm-B73-REFERENCE-NAM-5.0/GCF_902167145.1_Zm-B73-REFERENCE-NAM-5.0_genomic.chrom.sizes samtools -paired python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py RAMPAGE_in_B73_ears_Rep1-GSM8043174-pooled-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam SAMstats-RAMPAGE_in_B73_ears_Rep1-GSM8043174-pooled -bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Zea_mays-Zm-B73-REFERENCE-NAM-5.0/GCF_902167145.1_Zm-B73-REFERENCE-NAM-5.0_genomic.chrom.sizes samtools -paired python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py RAMPAGE_in_B73_endosperm_Rep1-GSM8043176-pooled-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam SAMstats-RAMPAGE_in_B73_endosperm_Rep1-GSM8043176-pooled -bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Zea_mays-Zm-B73-REFERENCE-NAM-5.0/GCF_902167145.1_Zm-B73-REFERENCE-NAM-5.0_genomic.chrom.sizes samtools -paired python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py RAMPAGE_in_B73_pollen_Rep1-GSM8043178-pooled-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam SAMstats-RAMPAGE_in_B73_pollen_Rep1-GSM8043178-pooled -bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Zea_mays-Zm-B73-REFERENCE-NAM-5.0/GCF_902167145.1_Zm-B73-REFERENCE-NAM-5.0_genomic.chrom.sizes samtools -paired python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py RAMPAGE_in_B73_roots_Rep1-GSM8043180-pooled-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam SAMstats-RAMPAGE_in_B73_roots_Rep1-GSM8043180-pooled -bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Zea_mays-Zm-B73-REFERENCE-NAM-5.0/GCF_902167145.1_Zm-B73-REFERENCE-NAM-5.0_genomic.chrom.sizes samtools -paired python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py RAMPAGE_in_NC350_coleoptilar_node_Rep1-GSM8043202-pooled-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam SAMstats-RAMPAGE_in_NC350_coleoptilar_node_Rep1-GSM8043202-pooled -bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Zea_mays-Zm-B73-REFERENCE-NAM-5.0/GCF_902167145.1_Zm-B73-REFERENCE-NAM-5.0_genomic.chrom.sizes samtools -paired python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py RAMPAGE_in_NC350_ears_Rep1-GSM8043204-pooled-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam SAMstats-RAMPAGE_in_NC350_ears_Rep1-GSM8043204-pooled -bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Zea_mays-Zm-B73-REFERENCE-NAM-5.0/GCF_902167145.1_Zm-B73-REFERENCE-NAM-5.0_genomic.chrom.sizes samtools -paired python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py RAMPAGE_in_NC350_endosperm_Rep1-GSM8043206-pooled-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam SAMstats-RAMPAGE_in_NC350_endosperm_Rep1-GSM8043206-pooled -bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Zea_mays-Zm-B73-REFERENCE-NAM-5.0/GCF_902167145.1_Zm-B73-REFERENCE-NAM-5.0_genomic.chrom.sizes samtools -paired python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py RAMPAGE_in_NC350_pollen_Rep1-GSM8043208-pooled-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam SAMstats-RAMPAGE_in_NC350_pollen_Rep1-GSM8043208-pooled -bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Zea_mays-Zm-B73-REFERENCE-NAM-5.0/GCF_902167145.1_Zm-B73-REFERENCE-NAM-5.0_genomic.chrom.sizes samtools -paired python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py RAMPAGE_in_NC350_roots_Rep1-GSM8043210-pooled-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam SAMstats-RAMPAGE_in_NC350_roots_Rep1-GSM8043210-pooled -bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Zea_mays-Zm-B73-REFERENCE-NAM-5.0/GCF_902167145.1_Zm-B73-REFERENCE-NAM-5.0_genomic.chrom.sizes samtools -paired python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py RAMPAGE_in_TIL11_coleoptilar_node_Rep1-GSM8043260-pooled-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam SAMstats-RAMPAGE_in_TIL11_coleoptilar_node_Rep1-GSM8043260-pooled -bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Zea_mays-Zm-B73-REFERENCE-NAM-5.0/GCF_902167145.1_Zm-B73-REFERENCE-NAM-5.0_genomic.chrom.sizes samtools -paired python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py RAMPAGE_in_TIL11_ears_Rep1-GSM8043262-pooled-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam SAMstats-RAMPAGE_in_TIL11_ears_Rep1-GSM8043262-pooled -bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Zea_mays-Zm-B73-REFERENCE-NAM-5.0/GCF_902167145.1_Zm-B73-REFERENCE-NAM-5.0_genomic.chrom.sizes samtools -paired python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py RAMPAGE_in_TIL11_pollen_Rep1-GSM8043264-pooled-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam SAMstats-RAMPAGE_in_TIL11_pollen_Rep1-GSM8043264-pooled -bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Zea_mays-Zm-B73-REFERENCE-NAM-5.0/GCF_902167145.1_Zm-B73-REFERENCE-NAM-5.0_genomic.chrom.sizes samtools -paired python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py RAMPAGE_in_W22_coleoptilar_node_Rep1-GSM8285413-pooled-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam SAMstats-RAMPAGE_in_W22_coleoptilar_node_Rep1-GSM8285413-pooled -bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Zea_mays-Zm-B73-REFERENCE-NAM-5.0/GCF_902167145.1_Zm-B73-REFERENCE-NAM-5.0_genomic.chrom.sizes samtools -paired python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py RAMPAGE_in_W22_ears_Rep1-GSM8285415-pooled-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam SAMstats-RAMPAGE_in_W22_ears_Rep1-GSM8285415-pooled -bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Zea_mays-Zm-B73-REFERENCE-NAM-5.0/GCF_902167145.1_Zm-B73-REFERENCE-NAM-5.0_genomic.chrom.sizes samtools -paired python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py RAMPAGE_in_W22_endosperm_Rep1-GSM8285417-pooled-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam SAMstats-RAMPAGE_in_W22_endosperm_Rep1-GSM8285417-pooled -bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Zea_mays-Zm-B73-REFERENCE-NAM-5.0/GCF_902167145.1_Zm-B73-REFERENCE-NAM-5.0_genomic.chrom.sizes samtools -paired python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py RAMPAGE_in_W22_pollen_Rep1-GSM8285419-pooled-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam SAMstats-RAMPAGE_in_W22_pollen_Rep1-GSM8285419-pooled -bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Zea_mays-Zm-B73-REFERENCE-NAM-5.0/GCF_902167145.1_Zm-B73-REFERENCE-NAM-5.0_genomic.chrom.sizes samtools -paired python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py RAMPAGE_in_W22_roots_Rep1-GSM8285421-pooled-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam SAMstats-RAMPAGE_in_W22_roots_Rep1-GSM8285421-pooled -bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Zea_mays-Zm-B73-REFERENCE-NAM-5.0/GCF_902167145.1_Zm-B73-REFERENCE-NAM-5.0_genomic.chrom.sizes samtools -paired