mkdir ME49.Bz.A-SRX9295974-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/Apicomplexa/Toxoplasma_gondii/STAR --outFileNamePrefix ME49.Bz.A-SRX9295974-STAR-2.5.3a/STAR-2.5.3a- --readFilesIn ME49.Bz.A-SRX9295974.end1.fastq.gz ME49.Bz.A-SRX9295974.end2.fastq.gz --sjdbGTFfile /oak/stanford/groups/akundaje/marinovg/genomes/Apicomplexa/Toxoplasma_gondii/Toxoplasma_gondii.ToxoDB-7.1.20.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 ME49.Bz.B-SRX9295975-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/Apicomplexa/Toxoplasma_gondii/STAR --outFileNamePrefix ME49.Bz.B-SRX9295975-STAR-2.5.3a/STAR-2.5.3a- --readFilesIn ME49.Bz.B-SRX9295975.end1.fastq.gz ME49.Bz.B-SRX9295975.end2.fastq.gz --sjdbGTFfile /oak/stanford/groups/akundaje/marinovg/genomes/Apicomplexa/Toxoplasma_gondii/Toxoplasma_gondii.ToxoDB-7.1.20.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 ME49.Tz.A-SRX9295976-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/Apicomplexa/Toxoplasma_gondii/STAR --outFileNamePrefix ME49.Tz.A-SRX9295976-STAR-2.5.3a/STAR-2.5.3a- --readFilesIn ME49.Tz.A-SRX9295976.end1.fastq.gz ME49.Tz.A-SRX9295976.end2.fastq.gz --sjdbGTFfile /oak/stanford/groups/akundaje/marinovg/genomes/Apicomplexa/Toxoplasma_gondii/Toxoplasma_gondii.ToxoDB-7.1.20.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 ME49.Tz.B-SRX9295977-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/Apicomplexa/Toxoplasma_gondii/STAR --outFileNamePrefix ME49.Tz.B-SRX9295977-STAR-2.5.3a/STAR-2.5.3a- --readFilesIn ME49.Tz.B-SRX9295977.end1.fastq.gz ME49.Tz.B-SRX9295977.end2.fastq.gz --sjdbGTFfile /oak/stanford/groups/akundaje/marinovg/genomes/Apicomplexa/Toxoplasma_gondii/Toxoplasma_gondii.ToxoDB-7.1.20.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 RH.Tz.A-SRX9295978-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/Apicomplexa/Toxoplasma_gondii/STAR --outFileNamePrefix RH.Tz.A-SRX9295978-STAR-2.5.3a/STAR-2.5.3a- --readFilesIn RH.Tz.A-SRX9295978.end1.fastq.gz RH.Tz.A-SRX9295978.end2.fastq.gz --sjdbGTFfile /oak/stanford/groups/akundaje/marinovg/genomes/Apicomplexa/Toxoplasma_gondii/Toxoplasma_gondii.ToxoDB-7.1.20.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 RH.Tz.B-SRX9295979-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/Apicomplexa/Toxoplasma_gondii/STAR --outFileNamePrefix RH.Tz.B-SRX9295979-STAR-2.5.3a/STAR-2.5.3a- --readFilesIn RH.Tz.B-SRX9295979.end1.fastq.gz RH.Tz.B-SRX9295979.end2.fastq.gz --sjdbGTFfile /oak/stanford/groups/akundaje/marinovg/genomes/Apicomplexa/Toxoplasma_gondii/Toxoplasma_gondii.ToxoDB-7.1.20.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