/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/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/STAR --outFileNamePrefix 120517_PINKERTON_0180_BC0RRPACXX_L2_CTTGTA-STAR-2.5.3a/STAR-2.5.3a- --readFilesIn 120517_PINKERTON_0180_BC0RRPACXX_L2_CTTGTA_1_pf.fastq.gz 120517_PINKERTON_0180_BC0RRPACXX_L2_CTTGTA_2_pf.fastq.gz --runThreadN 8 --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 --quantMode TranscriptomeSAM --outWigStrand Stranded --twopassMode Basic --twopass1readsN -1 --limitBAMsortRAM 250000000000
/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/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/STAR --outFileNamePrefix 120517_PINKERTON_0180_BC0RRPACXX_L2_GCCAAT-STAR-2.5.3a/STAR-2.5.3a- --readFilesIn 120517_PINKERTON_0180_BC0RRPACXX_L2_GCCAAT_1_pf.fastq.gz 120517_PINKERTON_0180_BC0RRPACXX_L2_GCCAAT_2_pf.fastq.gz --runThreadN 8 --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 --quantMode TranscriptomeSAM --outWigStrand Stranded --twopassMode Basic --twopass1readsN -1 --limitBAMsortRAM 250000000000
/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/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/STAR --outFileNamePrefix 120517_PINKERTON_0180_BC0RRPACXX_L2_TGACCA-STAR-2.5.3a/STAR-2.5.3a- --readFilesIn 120517_PINKERTON_0180_BC0RRPACXX_L2_TGACCA_1_pf.fastq.gz 120517_PINKERTON_0180_BC0RRPACXX_L2_TGACCA_2_pf.fastq.gz --runThreadN 8 --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 --quantMode TranscriptomeSAM --outWigStrand Stranded --twopassMode Basic --twopass1readsN -1 --limitBAMsortRAM 250000000000
/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/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/STAR --outFileNamePrefix 130403_MONK_0275_AC1Y6RACXX_L8_CCGTCC-STAR-2.5.3a/STAR-2.5.3a- --readFilesIn 130403_MONK_0275_AC1Y6RACXX_L8_CCGTCC_1_pf.fastq.gz 130403_MONK_0275_AC1Y6RACXX_L8_CCGTCC_2_pf.fastq.gz --runThreadN 8 --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 --quantMode TranscriptomeSAM --outWigStrand Stranded --twopassMode Basic --twopass1readsN -1 --limitBAMsortRAM 250000000000
/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/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/STAR --outFileNamePrefix 130403_MONK_0275_AC1Y6RACXX_L8_GTCCGC-STAR-2.5.3a/STAR-2.5.3a- --readFilesIn 130403_MONK_0275_AC1Y6RACXX_L8_GTCCGC_1_pf.fastq.gz 130403_MONK_0275_AC1Y6RACXX_L8_GTCCGC_2_pf.fastq.gz --runThreadN 8 --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 --quantMode TranscriptomeSAM --outWigStrand Stranded --twopassMode Basic --twopass1readsN -1 --limitBAMsortRAM 250000000000
/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/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/STAR --outFileNamePrefix 130403_MONK_0275_AC1Y6RACXX_L8_GTGAAA-STAR-2.5.3a/STAR-2.5.3a- --readFilesIn 130403_MONK_0275_AC1Y6RACXX_L8_GTGAAA_1_pf.fastq.gz 130403_MONK_0275_AC1Y6RACXX_L8_GTGAAA_2_pf.fastq.gz --runThreadN 8 --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 --quantMode TranscriptomeSAM --outWigStrand Stranded --twopassMode Basic --twopass1readsN -1 --limitBAMsortRAM 250000000000