mkdir RAMPAGE_in_B73_coleoptilar_node-pooled-STAR-2.5.3a; /oak/stanford/groups/akundaje/marinovg/programs/STAR-2.5.3a/bin/Linux_x86_64_static/STAR --limitSjdbInsertNsj 10000000 --genomeDir /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Zea_mays-Zm-B73-REFERENCE-NAM-5.0/STAR --outFileNamePrefix RAMPAGE_in_B73_coleoptilar_node-pooled-STAR-2.5.3a/STAR-2.5.3a- --readFilesIn RAMPAGE_in_B73_coleoptilar_node-pooled.end1.fastq.gz RAMPAGE_in_B73_coleoptilar_node-pooled.end2.fastq.gz --sjdbGTFfile /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.gtf --runThreadN 20 --outSAMunmapped Within --outFilterType BySJout --outSAMattributes NH HI AS NM MD --outFilterMultimapNmax 50 --outSAMstrandField intronMotif --outFilterMismatchNmax 999 --outFilterMismatchNoverReadLmax 0.04 --alignIntronMin 10 --alignIntronMax 1000000 --alignMatesGapMax 1000000 --alignSJoverhangMin 8 --alignSJDBoverhangMin 1 --sjdbScore 1 --readFilesCommand zcat --outSAMtype BAM SortedByCoordinate --outWigStrand Stranded  --twopassMode Basic --twopass1readsN -1 --limitBAMsortRAM 500000000000 
mkdir RAMPAGE_in_B73_ears_Rep1-GSM8043174-pooled-STAR-2.5.3a; /oak/stanford/groups/akundaje/marinovg/programs/STAR-2.5.3a/bin/Linux_x86_64_static/STAR --limitSjdbInsertNsj 10000000 --genomeDir /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Zea_mays-Zm-B73-REFERENCE-NAM-5.0/STAR --outFileNamePrefix RAMPAGE_in_B73_ears_Rep1-GSM8043174-pooled-STAR-2.5.3a/STAR-2.5.3a- --readFilesIn RAMPAGE_in_B73_ears_Rep1-GSM8043174-pooled.end1.fastq.gz RAMPAGE_in_B73_ears_Rep1-GSM8043174-pooled.end2.fastq.gz --sjdbGTFfile /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.gtf --runThreadN 20 --outSAMunmapped Within --outFilterType BySJout --outSAMattributes NH HI AS NM MD --outFilterMultimapNmax 50 --outSAMstrandField intronMotif --outFilterMismatchNmax 999 --outFilterMismatchNoverReadLmax 0.04 --alignIntronMin 10 --alignIntronMax 1000000 --alignMatesGapMax 1000000 --alignSJoverhangMin 8 --alignSJDBoverhangMin 1 --sjdbScore 1 --readFilesCommand zcat --outSAMtype BAM SortedByCoordinate --outWigStrand Stranded  --twopassMode Basic --twopass1readsN -1 --limitBAMsortRAM 500000000000 
mkdir RAMPAGE_in_B73_endosperm_Rep1-GSM8043176-pooled-STAR-2.5.3a; /oak/stanford/groups/akundaje/marinovg/programs/STAR-2.5.3a/bin/Linux_x86_64_static/STAR --limitSjdbInsertNsj 10000000 --genomeDir /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Zea_mays-Zm-B73-REFERENCE-NAM-5.0/STAR --outFileNamePrefix RAMPAGE_in_B73_endosperm_Rep1-GSM8043176-pooled-STAR-2.5.3a/STAR-2.5.3a- --readFilesIn RAMPAGE_in_B73_endosperm_Rep1-GSM8043176-pooled.end1.fastq.gz RAMPAGE_in_B73_endosperm_Rep1-GSM8043176-pooled.end2.fastq.gz --sjdbGTFfile /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.gtf --runThreadN 20 --outSAMunmapped Within --outFilterType BySJout --outSAMattributes NH HI AS NM MD --outFilterMultimapNmax 50 --outSAMstrandField intronMotif --outFilterMismatchNmax 999 --outFilterMismatchNoverReadLmax 0.04 --alignIntronMin 10 --alignIntronMax 1000000 --alignMatesGapMax 1000000 --alignSJoverhangMin 8 --alignSJDBoverhangMin 1 --sjdbScore 1 --readFilesCommand zcat --outSAMtype BAM SortedByCoordinate --outWigStrand Stranded  --twopassMode Basic --twopass1readsN -1 --limitBAMsortRAM 500000000000 
mkdir RAMPAGE_in_B73_pollen_Rep1-GSM8043178-pooled-STAR-2.5.3a; /oak/stanford/groups/akundaje/marinovg/programs/STAR-2.5.3a/bin/Linux_x86_64_static/STAR --limitSjdbInsertNsj 10000000 --genomeDir /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Zea_mays-Zm-B73-REFERENCE-NAM-5.0/STAR --outFileNamePrefix RAMPAGE_in_B73_pollen_Rep1-GSM8043178-pooled-STAR-2.5.3a/STAR-2.5.3a- --readFilesIn RAMPAGE_in_B73_pollen_Rep1-GSM8043178-pooled.end1.fastq.gz RAMPAGE_in_B73_pollen_Rep1-GSM8043178-pooled.end2.fastq.gz --sjdbGTFfile /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.gtf --runThreadN 20 --outSAMunmapped Within --outFilterType BySJout --outSAMattributes NH HI AS NM MD --outFilterMultimapNmax 50 --outSAMstrandField intronMotif --outFilterMismatchNmax 999 --outFilterMismatchNoverReadLmax 0.04 --alignIntronMin 10 --alignIntronMax 1000000 --alignMatesGapMax 1000000 --alignSJoverhangMin 8 --alignSJDBoverhangMin 1 --sjdbScore 1 --readFilesCommand zcat --outSAMtype BAM SortedByCoordinate --outWigStrand Stranded  --twopassMode Basic --twopass1readsN -1 --limitBAMsortRAM 500000000000 
mkdir RAMPAGE_in_B73_roots_Rep1-GSM8043180-pooled-STAR-2.5.3a; /oak/stanford/groups/akundaje/marinovg/programs/STAR-2.5.3a/bin/Linux_x86_64_static/STAR --limitSjdbInsertNsj 10000000 --genomeDir /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Zea_mays-Zm-B73-REFERENCE-NAM-5.0/STAR --outFileNamePrefix RAMPAGE_in_B73_roots_Rep1-GSM8043180-pooled-STAR-2.5.3a/STAR-2.5.3a- --readFilesIn RAMPAGE_in_B73_roots_Rep1-GSM8043180-pooled.end1.fastq.gz RAMPAGE_in_B73_roots_Rep1-GSM8043180-pooled.end2.fastq.gz --sjdbGTFfile /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.gtf --runThreadN 20 --outSAMunmapped Within --outFilterType BySJout --outSAMattributes NH HI AS NM MD --outFilterMultimapNmax 50 --outSAMstrandField intronMotif --outFilterMismatchNmax 999 --outFilterMismatchNoverReadLmax 0.04 --alignIntronMin 10 --alignIntronMax 1000000 --alignMatesGapMax 1000000 --alignSJoverhangMin 8 --alignSJDBoverhangMin 1 --sjdbScore 1 --readFilesCommand zcat --outSAMtype BAM SortedByCoordinate --outWigStrand Stranded  --twopassMode Basic --twopass1readsN -1 --limitBAMsortRAM 500000000000 
mkdir RAMPAGE_in_NC350_coleoptilar_node_Rep1-GSM8043202-pooled-STAR-2.5.3a; /oak/stanford/groups/akundaje/marinovg/programs/STAR-2.5.3a/bin/Linux_x86_64_static/STAR --limitSjdbInsertNsj 10000000 --genomeDir /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Zea_mays-Zm-B73-REFERENCE-NAM-5.0/STAR --outFileNamePrefix RAMPAGE_in_NC350_coleoptilar_node_Rep1-GSM8043202-pooled-STAR-2.5.3a/STAR-2.5.3a- --readFilesIn RAMPAGE_in_NC350_coleoptilar_node_Rep1-GSM8043202-pooled.end1.fastq.gz RAMPAGE_in_NC350_coleoptilar_node_Rep1-GSM8043202-pooled.end2.fastq.gz --sjdbGTFfile /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.gtf --runThreadN 20 --outSAMunmapped Within --outFilterType BySJout --outSAMattributes NH HI AS NM MD --outFilterMultimapNmax 50 --outSAMstrandField intronMotif --outFilterMismatchNmax 999 --outFilterMismatchNoverReadLmax 0.04 --alignIntronMin 10 --alignIntronMax 1000000 --alignMatesGapMax 1000000 --alignSJoverhangMin 8 --alignSJDBoverhangMin 1 --sjdbScore 1 --readFilesCommand zcat --outSAMtype BAM SortedByCoordinate --outWigStrand Stranded  --twopassMode Basic --twopass1readsN -1 --limitBAMsortRAM 500000000000 
mkdir RAMPAGE_in_NC350_ears_Rep1-GSM8043204-pooled-STAR-2.5.3a; /oak/stanford/groups/akundaje/marinovg/programs/STAR-2.5.3a/bin/Linux_x86_64_static/STAR --limitSjdbInsertNsj 10000000 --genomeDir /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Zea_mays-Zm-B73-REFERENCE-NAM-5.0/STAR --outFileNamePrefix RAMPAGE_in_NC350_ears_Rep1-GSM8043204-pooled-STAR-2.5.3a/STAR-2.5.3a- --readFilesIn RAMPAGE_in_NC350_ears_Rep1-GSM8043204-pooled.end1.fastq.gz RAMPAGE_in_NC350_ears_Rep1-GSM8043204-pooled.end2.fastq.gz --sjdbGTFfile /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.gtf --runThreadN 20 --outSAMunmapped Within --outFilterType BySJout --outSAMattributes NH HI AS NM MD --outFilterMultimapNmax 50 --outSAMstrandField intronMotif --outFilterMismatchNmax 999 --outFilterMismatchNoverReadLmax 0.04 --alignIntronMin 10 --alignIntronMax 1000000 --alignMatesGapMax 1000000 --alignSJoverhangMin 8 --alignSJDBoverhangMin 1 --sjdbScore 1 --readFilesCommand zcat --outSAMtype BAM SortedByCoordinate --outWigStrand Stranded  --twopassMode Basic --twopass1readsN -1 --limitBAMsortRAM 500000000000 
mkdir RAMPAGE_in_NC350_endosperm_Rep1-GSM8043206-pooled-STAR-2.5.3a; /oak/stanford/groups/akundaje/marinovg/programs/STAR-2.5.3a/bin/Linux_x86_64_static/STAR --limitSjdbInsertNsj 10000000 --genomeDir /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Zea_mays-Zm-B73-REFERENCE-NAM-5.0/STAR --outFileNamePrefix RAMPAGE_in_NC350_endosperm_Rep1-GSM8043206-pooled-STAR-2.5.3a/STAR-2.5.3a- --readFilesIn RAMPAGE_in_NC350_endosperm_Rep1-GSM8043206-pooled.end1.fastq.gz RAMPAGE_in_NC350_endosperm_Rep1-GSM8043206-pooled.end2.fastq.gz --sjdbGTFfile /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.gtf --runThreadN 20 --outSAMunmapped Within --outFilterType BySJout --outSAMattributes NH HI AS NM MD --outFilterMultimapNmax 50 --outSAMstrandField intronMotif --outFilterMismatchNmax 999 --outFilterMismatchNoverReadLmax 0.04 --alignIntronMin 10 --alignIntronMax 1000000 --alignMatesGapMax 1000000 --alignSJoverhangMin 8 --alignSJDBoverhangMin 1 --sjdbScore 1 --readFilesCommand zcat --outSAMtype BAM SortedByCoordinate --outWigStrand Stranded  --twopassMode Basic --twopass1readsN -1 --limitBAMsortRAM 500000000000 
mkdir RAMPAGE_in_NC350_pollen_Rep1-GSM8043208-pooled-STAR-2.5.3a; /oak/stanford/groups/akundaje/marinovg/programs/STAR-2.5.3a/bin/Linux_x86_64_static/STAR --limitSjdbInsertNsj 10000000 --genomeDir /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Zea_mays-Zm-B73-REFERENCE-NAM-5.0/STAR --outFileNamePrefix RAMPAGE_in_NC350_pollen_Rep1-GSM8043208-pooled-STAR-2.5.3a/STAR-2.5.3a- --readFilesIn RAMPAGE_in_NC350_pollen_Rep1-GSM8043208-pooled.end1.fastq.gz RAMPAGE_in_NC350_pollen_Rep1-GSM8043208-pooled.end2.fastq.gz --sjdbGTFfile /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.gtf --runThreadN 20 --outSAMunmapped Within --outFilterType BySJout --outSAMattributes NH HI AS NM MD --outFilterMultimapNmax 50 --outSAMstrandField intronMotif --outFilterMismatchNmax 999 --outFilterMismatchNoverReadLmax 0.04 --alignIntronMin 10 --alignIntronMax 1000000 --alignMatesGapMax 1000000 --alignSJoverhangMin 8 --alignSJDBoverhangMin 1 --sjdbScore 1 --readFilesCommand zcat --outSAMtype BAM SortedByCoordinate --outWigStrand Stranded  --twopassMode Basic --twopass1readsN -1 --limitBAMsortRAM 500000000000 
mkdir RAMPAGE_in_NC350_roots_Rep1-GSM8043210-pooled-STAR-2.5.3a; /oak/stanford/groups/akundaje/marinovg/programs/STAR-2.5.3a/bin/Linux_x86_64_static/STAR --limitSjdbInsertNsj 10000000 --genomeDir /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Zea_mays-Zm-B73-REFERENCE-NAM-5.0/STAR --outFileNamePrefix RAMPAGE_in_NC350_roots_Rep1-GSM8043210-pooled-STAR-2.5.3a/STAR-2.5.3a- --readFilesIn RAMPAGE_in_NC350_roots_Rep1-GSM8043210-pooled.end1.fastq.gz RAMPAGE_in_NC350_roots_Rep1-GSM8043210-pooled.end2.fastq.gz --sjdbGTFfile /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.gtf --runThreadN 20 --outSAMunmapped Within --outFilterType BySJout --outSAMattributes NH HI AS NM MD --outFilterMultimapNmax 50 --outSAMstrandField intronMotif --outFilterMismatchNmax 999 --outFilterMismatchNoverReadLmax 0.04 --alignIntronMin 10 --alignIntronMax 1000000 --alignMatesGapMax 1000000 --alignSJoverhangMin 8 --alignSJDBoverhangMin 1 --sjdbScore 1 --readFilesCommand zcat --outSAMtype BAM SortedByCoordinate --outWigStrand Stranded  --twopassMode Basic --twopass1readsN -1 --limitBAMsortRAM 500000000000 
mkdir RAMPAGE_in_TIL11_coleoptilar_node_Rep1-GSM8043260-pooled-STAR-2.5.3a; /oak/stanford/groups/akundaje/marinovg/programs/STAR-2.5.3a/bin/Linux_x86_64_static/STAR --limitSjdbInsertNsj 10000000 --genomeDir /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Zea_mays-Zm-B73-REFERENCE-NAM-5.0/STAR --outFileNamePrefix RAMPAGE_in_TIL11_coleoptilar_node_Rep1-GSM8043260-pooled-STAR-2.5.3a/STAR-2.5.3a- --readFilesIn RAMPAGE_in_TIL11_coleoptilar_node_Rep1-GSM8043260-pooled.end1.fastq.gz RAMPAGE_in_TIL11_coleoptilar_node_Rep1-GSM8043260-pooled.end2.fastq.gz --sjdbGTFfile /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.gtf --runThreadN 20 --outSAMunmapped Within --outFilterType BySJout --outSAMattributes NH HI AS NM MD --outFilterMultimapNmax 50 --outSAMstrandField intronMotif --outFilterMismatchNmax 999 --outFilterMismatchNoverReadLmax 0.04 --alignIntronMin 10 --alignIntronMax 1000000 --alignMatesGapMax 1000000 --alignSJoverhangMin 8 --alignSJDBoverhangMin 1 --sjdbScore 1 --readFilesCommand zcat --outSAMtype BAM SortedByCoordinate --outWigStrand Stranded  --twopassMode Basic --twopass1readsN -1 --limitBAMsortRAM 500000000000 
mkdir RAMPAGE_in_TIL11_ears_Rep1-GSM8043262-pooled-STAR-2.5.3a; /oak/stanford/groups/akundaje/marinovg/programs/STAR-2.5.3a/bin/Linux_x86_64_static/STAR --limitSjdbInsertNsj 10000000 --genomeDir /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Zea_mays-Zm-B73-REFERENCE-NAM-5.0/STAR --outFileNamePrefix RAMPAGE_in_TIL11_ears_Rep1-GSM8043262-pooled-STAR-2.5.3a/STAR-2.5.3a- --readFilesIn RAMPAGE_in_TIL11_ears_Rep1-GSM8043262-pooled.end1.fastq.gz RAMPAGE_in_TIL11_ears_Rep1-GSM8043262-pooled.end2.fastq.gz --sjdbGTFfile /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.gtf --runThreadN 20 --outSAMunmapped Within --outFilterType BySJout --outSAMattributes NH HI AS NM MD --outFilterMultimapNmax 50 --outSAMstrandField intronMotif --outFilterMismatchNmax 999 --outFilterMismatchNoverReadLmax 0.04 --alignIntronMin 10 --alignIntronMax 1000000 --alignMatesGapMax 1000000 --alignSJoverhangMin 8 --alignSJDBoverhangMin 1 --sjdbScore 1 --readFilesCommand zcat --outSAMtype BAM SortedByCoordinate --outWigStrand Stranded  --twopassMode Basic --twopass1readsN -1 --limitBAMsortRAM 500000000000 
mkdir RAMPAGE_in_TIL11_pollen_Rep1-GSM8043264-pooled-STAR-2.5.3a; /oak/stanford/groups/akundaje/marinovg/programs/STAR-2.5.3a/bin/Linux_x86_64_static/STAR --limitSjdbInsertNsj 10000000 --genomeDir /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Zea_mays-Zm-B73-REFERENCE-NAM-5.0/STAR --outFileNamePrefix RAMPAGE_in_TIL11_pollen_Rep1-GSM8043264-pooled-STAR-2.5.3a/STAR-2.5.3a- --readFilesIn RAMPAGE_in_TIL11_pollen_Rep1-GSM8043264-pooled.end1.fastq.gz RAMPAGE_in_TIL11_pollen_Rep1-GSM8043264-pooled.end2.fastq.gz --sjdbGTFfile /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.gtf --runThreadN 20 --outSAMunmapped Within --outFilterType BySJout --outSAMattributes NH HI AS NM MD --outFilterMultimapNmax 50 --outSAMstrandField intronMotif --outFilterMismatchNmax 999 --outFilterMismatchNoverReadLmax 0.04 --alignIntronMin 10 --alignIntronMax 1000000 --alignMatesGapMax 1000000 --alignSJoverhangMin 8 --alignSJDBoverhangMin 1 --sjdbScore 1 --readFilesCommand zcat --outSAMtype BAM SortedByCoordinate --outWigStrand Stranded  --twopassMode Basic --twopass1readsN -1 --limitBAMsortRAM 500000000000 
mkdir RAMPAGE_in_W22_coleoptilar_node_Rep1-GSM8285413-pooled-STAR-2.5.3a; /oak/stanford/groups/akundaje/marinovg/programs/STAR-2.5.3a/bin/Linux_x86_64_static/STAR --limitSjdbInsertNsj 10000000 --genomeDir /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Zea_mays-Zm-B73-REFERENCE-NAM-5.0/STAR --outFileNamePrefix RAMPAGE_in_W22_coleoptilar_node_Rep1-GSM8285413-pooled-STAR-2.5.3a/STAR-2.5.3a- --readFilesIn RAMPAGE_in_W22_coleoptilar_node_Rep1-GSM8285413-pooled.end1.fastq.gz RAMPAGE_in_W22_coleoptilar_node_Rep1-GSM8285413-pooled.end2.fastq.gz --sjdbGTFfile /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.gtf --runThreadN 20 --outSAMunmapped Within --outFilterType BySJout --outSAMattributes NH HI AS NM MD --outFilterMultimapNmax 50 --outSAMstrandField intronMotif --outFilterMismatchNmax 999 --outFilterMismatchNoverReadLmax 0.04 --alignIntronMin 10 --alignIntronMax 1000000 --alignMatesGapMax 1000000 --alignSJoverhangMin 8 --alignSJDBoverhangMin 1 --sjdbScore 1 --readFilesCommand zcat --outSAMtype BAM SortedByCoordinate --outWigStrand Stranded  --twopassMode Basic --twopass1readsN -1 --limitBAMsortRAM 500000000000 
mkdir RAMPAGE_in_W22_ears_Rep1-GSM8285415-pooled-STAR-2.5.3a; /oak/stanford/groups/akundaje/marinovg/programs/STAR-2.5.3a/bin/Linux_x86_64_static/STAR --limitSjdbInsertNsj 10000000 --genomeDir /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Zea_mays-Zm-B73-REFERENCE-NAM-5.0/STAR --outFileNamePrefix RAMPAGE_in_W22_ears_Rep1-GSM8285415-pooled-STAR-2.5.3a/STAR-2.5.3a- --readFilesIn RAMPAGE_in_W22_ears_Rep1-GSM8285415-pooled.end1.fastq.gz RAMPAGE_in_W22_ears_Rep1-GSM8285415-pooled.end2.fastq.gz --sjdbGTFfile /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.gtf --runThreadN 20 --outSAMunmapped Within --outFilterType BySJout --outSAMattributes NH HI AS NM MD --outFilterMultimapNmax 50 --outSAMstrandField intronMotif --outFilterMismatchNmax 999 --outFilterMismatchNoverReadLmax 0.04 --alignIntronMin 10 --alignIntronMax 1000000 --alignMatesGapMax 1000000 --alignSJoverhangMin 8 --alignSJDBoverhangMin 1 --sjdbScore 1 --readFilesCommand zcat --outSAMtype BAM SortedByCoordinate --outWigStrand Stranded  --twopassMode Basic --twopass1readsN -1 --limitBAMsortRAM 500000000000 
mkdir RAMPAGE_in_W22_endosperm_Rep1-GSM8285417-pooled-STAR-2.5.3a; /oak/stanford/groups/akundaje/marinovg/programs/STAR-2.5.3a/bin/Linux_x86_64_static/STAR --limitSjdbInsertNsj 10000000 --genomeDir /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Zea_mays-Zm-B73-REFERENCE-NAM-5.0/STAR --outFileNamePrefix RAMPAGE_in_W22_endosperm_Rep1-GSM8285417-pooled-STAR-2.5.3a/STAR-2.5.3a- --readFilesIn RAMPAGE_in_W22_endosperm_Rep1-GSM8285417-pooled.end1.fastq.gz RAMPAGE_in_W22_endosperm_Rep1-GSM8285417-pooled.end2.fastq.gz --sjdbGTFfile /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.gtf --runThreadN 20 --outSAMunmapped Within --outFilterType BySJout --outSAMattributes NH HI AS NM MD --outFilterMultimapNmax 50 --outSAMstrandField intronMotif --outFilterMismatchNmax 999 --outFilterMismatchNoverReadLmax 0.04 --alignIntronMin 10 --alignIntronMax 1000000 --alignMatesGapMax 1000000 --alignSJoverhangMin 8 --alignSJDBoverhangMin 1 --sjdbScore 1 --readFilesCommand zcat --outSAMtype BAM SortedByCoordinate --outWigStrand Stranded  --twopassMode Basic --twopass1readsN -1 --limitBAMsortRAM 500000000000 
mkdir RAMPAGE_in_W22_pollen_Rep1-GSM8285419-pooled-STAR-2.5.3a; /oak/stanford/groups/akundaje/marinovg/programs/STAR-2.5.3a/bin/Linux_x86_64_static/STAR --limitSjdbInsertNsj 10000000 --genomeDir /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Zea_mays-Zm-B73-REFERENCE-NAM-5.0/STAR --outFileNamePrefix RAMPAGE_in_W22_pollen_Rep1-GSM8285419-pooled-STAR-2.5.3a/STAR-2.5.3a- --readFilesIn RAMPAGE_in_W22_pollen_Rep1-GSM8285419-pooled.end1.fastq.gz RAMPAGE_in_W22_pollen_Rep1-GSM8285419-pooled.end2.fastq.gz --sjdbGTFfile /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.gtf --runThreadN 20 --outSAMunmapped Within --outFilterType BySJout --outSAMattributes NH HI AS NM MD --outFilterMultimapNmax 50 --outSAMstrandField intronMotif --outFilterMismatchNmax 999 --outFilterMismatchNoverReadLmax 0.04 --alignIntronMin 10 --alignIntronMax 1000000 --alignMatesGapMax 1000000 --alignSJoverhangMin 8 --alignSJDBoverhangMin 1 --sjdbScore 1 --readFilesCommand zcat --outSAMtype BAM SortedByCoordinate --outWigStrand Stranded  --twopassMode Basic --twopass1readsN -1 --limitBAMsortRAM 500000000000 
mkdir RAMPAGE_in_W22_roots_Rep1-GSM8285421-pooled-STAR-2.5.3a; /oak/stanford/groups/akundaje/marinovg/programs/STAR-2.5.3a/bin/Linux_x86_64_static/STAR --limitSjdbInsertNsj 10000000 --genomeDir /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Zea_mays-Zm-B73-REFERENCE-NAM-5.0/STAR --outFileNamePrefix RAMPAGE_in_W22_roots_Rep1-GSM8285421-pooled-STAR-2.5.3a/STAR-2.5.3a- --readFilesIn RAMPAGE_in_W22_roots_Rep1-GSM8285421-pooled.end1.fastq.gz RAMPAGE_in_W22_roots_Rep1-GSM8285421-pooled.end2.fastq.gz --sjdbGTFfile /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.gtf --runThreadN 20 --outSAMunmapped Within --outFilterType BySJout --outSAMattributes NH HI AS NM MD --outFilterMultimapNmax 50 --outSAMstrandField intronMotif --outFilterMismatchNmax 999 --outFilterMismatchNoverReadLmax 0.04 --alignIntronMin 10 --alignIntronMax 1000000 --alignMatesGapMax 1000000 --alignSJoverhangMin 8 --alignSJDBoverhangMin 1 --sjdbScore 1 --readFilesCommand zcat --outSAMtype BAM SortedByCoordinate --outWigStrand Stranded  --twopassMode Basic --twopass1readsN -1 --limitBAMsortRAM 500000000000