mkdir Selaginella_moellendorffii_stem_leaves_5GRO-seq_r1-GSM7439248-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/Selaginella_moellendorffii/STAR --outFileNamePrefix Selaginella_moellendorffii_stem_leaves_5GRO-seq_r1-GSM7439248-STAR-2.5.3a/STAR-2.5.3a- --readFilesIn Selaginella_moellendorffii_stem_leaves_5GRO-seq_r1-GSM7439248/SRR24798043.fastq.gz --sjdbGTFfile /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Selaginella_moellendorffii/Selaginella_moellendorffii.v1.0.19.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 Selaginella_moellendorffii_stem_leaves_GRO-seq_r1-GSM7439251-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/Selaginella_moellendorffii/STAR --outFileNamePrefix Selaginella_moellendorffii_stem_leaves_GRO-seq_r1-GSM7439251-STAR-2.5.3a/STAR-2.5.3a- --readFilesIn Selaginella_moellendorffii_stem_leaves_GRO-seq_r1-GSM7439251/SRR24798040.fastq.gz --sjdbGTFfile /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Selaginella_moellendorffii/Selaginella_moellendorffii.v1.0.19.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