mkdir Total_RNA_0hpf-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/Echinodermata/Strongylocentrotus_purpuratus-Spur_5.0/STAR --outFileNamePrefix Total_RNA_0hpf-STAR-2.5.3a/STAR-2.5.3a- --readFilesIn Total_RNA_0hpf.fastq.gz --sjdbGTFfile /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Echinodermata/Strongylocentrotus_purpuratus-Spur_5.0/Strongylocentrotus_purpuratus-Spur_5.0.fixed.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 Total_RNA_12hpf-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/Echinodermata/Strongylocentrotus_purpuratus-Spur_5.0/STAR --outFileNamePrefix Total_RNA_12hpf-STAR-2.5.3a/STAR-2.5.3a- --readFilesIn Total_RNA_12hpf.fastq.gz --sjdbGTFfile /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Echinodermata/Strongylocentrotus_purpuratus-Spur_5.0/Strongylocentrotus_purpuratus-Spur_5.0.fixed.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 Total_RNA_18hpf-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/Echinodermata/Strongylocentrotus_purpuratus-Spur_5.0/STAR --outFileNamePrefix Total_RNA_18hpf-STAR-2.5.3a/STAR-2.5.3a- --readFilesIn Total_RNA_18hpf.fastq.gz --sjdbGTFfile /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Echinodermata/Strongylocentrotus_purpuratus-Spur_5.0/Strongylocentrotus_purpuratus-Spur_5.0.fixed.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 Total_RNA_24hpf-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/Echinodermata/Strongylocentrotus_purpuratus-Spur_5.0/STAR --outFileNamePrefix Total_RNA_24hpf-STAR-2.5.3a/STAR-2.5.3a- --readFilesIn Total_RNA_24hpf.fastq.gz --sjdbGTFfile /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Echinodermata/Strongylocentrotus_purpuratus-Spur_5.0/Strongylocentrotus_purpuratus-Spur_5.0.fixed.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 Total_RNA_30hpf-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/Echinodermata/Strongylocentrotus_purpuratus-Spur_5.0/STAR --outFileNamePrefix Total_RNA_30hpf-STAR-2.5.3a/STAR-2.5.3a- --readFilesIn Total_RNA_30hpf.fastq.gz --sjdbGTFfile /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Echinodermata/Strongylocentrotus_purpuratus-Spur_5.0/Strongylocentrotus_purpuratus-Spur_5.0.fixed.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 Total_RNA_36hpf-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/Echinodermata/Strongylocentrotus_purpuratus-Spur_5.0/STAR --outFileNamePrefix Total_RNA_36hpf-STAR-2.5.3a/STAR-2.5.3a- --readFilesIn Total_RNA_36hpf.fastq.gz --sjdbGTFfile /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Echinodermata/Strongylocentrotus_purpuratus-Spur_5.0/Strongylocentrotus_purpuratus-Spur_5.0.fixed.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 Total_RNA_42hpf-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/Echinodermata/Strongylocentrotus_purpuratus-Spur_5.0/STAR --outFileNamePrefix Total_RNA_42hpf-STAR-2.5.3a/STAR-2.5.3a- --readFilesIn Total_RNA_42hpf.fastq.gz --sjdbGTFfile /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Echinodermata/Strongylocentrotus_purpuratus-Spur_5.0/Strongylocentrotus_purpuratus-Spur_5.0.fixed.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 Total_RNA_48hpf-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/Echinodermata/Strongylocentrotus_purpuratus-Spur_5.0/STAR --outFileNamePrefix Total_RNA_48hpf-STAR-2.5.3a/STAR-2.5.3a- --readFilesIn Total_RNA_48hpf.fastq.gz --sjdbGTFfile /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Echinodermata/Strongylocentrotus_purpuratus-Spur_5.0/Strongylocentrotus_purpuratus-Spur_5.0.fixed.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 Total_RNA_6hpf-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/Echinodermata/Strongylocentrotus_purpuratus-Spur_5.0/STAR --outFileNamePrefix Total_RNA_6hpf-STAR-2.5.3a/STAR-2.5.3a- --readFilesIn Total_RNA_6hpf.fastq.gz --sjdbGTFfile /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Echinodermata/Strongylocentrotus_purpuratus-Spur_5.0/Strongylocentrotus_purpuratus-Spur_5.0.fixed.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