mkdir TSS_tur1delta_30E_merged-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/Fungi/Cryptococcus_neoformans/STAR --outFileNamePrefix TSS_tur1delta_30E_merged-STAR-2.5.3a/STAR-2.5.3a- --readFilesIn TSS_tur1delta_30E_merged.fastq.gz --sjdbGTFfile /oak/stanford/groups/akundaje/marinovg/genomes/Fungi/Cryptococcus_neoformans/Cryptococcus_neoformans.GCA_000091045.1.20.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 TSS_tur1delta_30E_rep_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/Fungi/Cryptococcus_neoformans/STAR --outFileNamePrefix TSS_tur1delta_30E_rep_1-STAR-2.5.3a/STAR-2.5.3a- --readFilesIn TSS_tur1delta_30E_rep_1.fastq.gz --sjdbGTFfile /oak/stanford/groups/akundaje/marinovg/genomes/Fungi/Cryptococcus_neoformans/Cryptococcus_neoformans.GCA_000091045.1.20.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 TSS_tur1delta_30E_rep_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/Fungi/Cryptococcus_neoformans/STAR --outFileNamePrefix TSS_tur1delta_30E_rep_2-STAR-2.5.3a/STAR-2.5.3a- --readFilesIn TSS_tur1delta_30E_rep_2.fastq.gz --sjdbGTFfile /oak/stanford/groups/akundaje/marinovg/genomes/Fungi/Cryptococcus_neoformans/Cryptococcus_neoformans.GCA_000091045.1.20.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 TSS_tur1delta_30E_rep_3-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/Fungi/Cryptococcus_neoformans/STAR --outFileNamePrefix TSS_tur1delta_30E_rep_3-STAR-2.5.3a/STAR-2.5.3a- --readFilesIn TSS_tur1delta_30E_rep_3.fastq.gz --sjdbGTFfile /oak/stanford/groups/akundaje/marinovg/genomes/Fungi/Cryptococcus_neoformans/Cryptococcus_neoformans.GCA_000091045.1.20.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 TSS_tur1delta_30S_merged-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/Fungi/Cryptococcus_neoformans/STAR --outFileNamePrefix TSS_tur1delta_30S_merged-STAR-2.5.3a/STAR-2.5.3a- --readFilesIn TSS_tur1delta_30S_merged.fastq.gz --sjdbGTFfile /oak/stanford/groups/akundaje/marinovg/genomes/Fungi/Cryptococcus_neoformans/Cryptococcus_neoformans.GCA_000091045.1.20.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 TSS_tur1delta_30S_rep_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/Fungi/Cryptococcus_neoformans/STAR --outFileNamePrefix TSS_tur1delta_30S_rep_1-STAR-2.5.3a/STAR-2.5.3a- --readFilesIn TSS_tur1delta_30S_rep_1.fastq.gz --sjdbGTFfile /oak/stanford/groups/akundaje/marinovg/genomes/Fungi/Cryptococcus_neoformans/Cryptococcus_neoformans.GCA_000091045.1.20.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 TSS_tur1delta_30S_rep_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/Fungi/Cryptococcus_neoformans/STAR --outFileNamePrefix TSS_tur1delta_30S_rep_2-STAR-2.5.3a/STAR-2.5.3a- --readFilesIn TSS_tur1delta_30S_rep_2.fastq.gz --sjdbGTFfile /oak/stanford/groups/akundaje/marinovg/genomes/Fungi/Cryptococcus_neoformans/Cryptococcus_neoformans.GCA_000091045.1.20.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 TSS_tur1delta_30S_rep_3-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/Fungi/Cryptococcus_neoformans/STAR --outFileNamePrefix TSS_tur1delta_30S_rep_3-STAR-2.5.3a/STAR-2.5.3a- --readFilesIn TSS_tur1delta_30S_rep_3.fastq.gz --sjdbGTFfile /oak/stanford/groups/akundaje/marinovg/genomes/Fungi/Cryptococcus_neoformans/Cryptococcus_neoformans.GCA_000091045.1.20.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