mkdir HARMI-1-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/Metazoa/Insects/Helicoverpa_armigera-Harm_1.0/STAR --outFileNamePrefix HARMI-1-STAR-2.5.3a/STAR-2.5.3a- --readFilesIn HARMI-1.end1.fastq.gz HARMI-1.end2.fastq.gz --sjdbGTFfile /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Insects/Helicoverpa_armigera-Harm_1.0/GCA_002156985.1_Harm_1.0_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 HARMI-2-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/Metazoa/Insects/Helicoverpa_armigera-Harm_1.0/STAR --outFileNamePrefix HARMI-2-STAR-2.5.3a/STAR-2.5.3a- --readFilesIn HARMI-2.end1.fastq.gz HARMI-2.end2.fastq.gz --sjdbGTFfile /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Insects/Helicoverpa_armigera-Harm_1.0/GCA_002156985.1_Harm_1.0_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