mkdir Adipose-pooled-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/Birds/Gallus_gallus-GRCg6a/STAR --outFileNamePrefix Adipose-pooled-STAR-2.5.3a/STAR-2.5.3a- --readFilesIn Adipose-pooled.end1.fastq.gz Adipose-pooled.end2.fastq.gz --sjdbGTFfile /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Birds/Gallus_gallus-GRCg6a/Gallus_gallus.GRCg6a.102.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 BoneMarrow-pooled-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/Birds/Gallus_gallus-GRCg6a/STAR --outFileNamePrefix BoneMarrow-pooled-STAR-2.5.3a/STAR-2.5.3a- --readFilesIn BoneMarrow.end1.fastq.gz BoneMarrow.end2.fastq.gz --sjdbGTFfile /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Birds/Gallus_gallus-GRCg6a/Gallus_gallus.GRCg6a.102.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 BrainCortex-pooled-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/Birds/Gallus_gallus-GRCg6a/STAR --outFileNamePrefix BrainCortex-pooled-STAR-2.5.3a/STAR-2.5.3a- --readFilesIn BrainCortex.end1.fastq.gz BrainCortex.end2.fastq.gz --sjdbGTFfile /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Birds/Gallus_gallus-GRCg6a/Gallus_gallus.GRCg6a.102.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 Cecum-pooled-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/Birds/Gallus_gallus-GRCg6a/STAR --outFileNamePrefix Cecum-pooled-STAR-2.5.3a/STAR-2.5.3a- --readFilesIn Cecum.end1.fastq.gz Cecum.end2.fastq.gz --sjdbGTFfile /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Birds/Gallus_gallus-GRCg6a/Gallus_gallus.GRCg6a.102.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 Cerebellum-pooled-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/Birds/Gallus_gallus-GRCg6a/STAR --outFileNamePrefix Cerebellum-pooled-STAR-2.5.3a/STAR-2.5.3a- --readFilesIn Cerebellum.end1.fastq.gz Cerebellum.end2.fastq.gz --sjdbGTFfile /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Birds/Gallus_gallus-GRCg6a/Gallus_gallus.GRCg6a.102.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 Colon-pooled-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/Birds/Gallus_gallus-GRCg6a/STAR --outFileNamePrefix Colon-pooled-STAR-2.5.3a/STAR-2.5.3a- --readFilesIn Colon.end1.fastq.gz Colon.end2.fastq.gz --sjdbGTFfile /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Birds/Gallus_gallus-GRCg6a/Gallus_gallus.GRCg6a.102.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 Duodenum-pooled-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/Birds/Gallus_gallus-GRCg6a/STAR --outFileNamePrefix Duodenum-pooled-STAR-2.5.3a/STAR-2.5.3a- --readFilesIn Duodenum.end1.fastq.gz.end1.fastq.gz Duodenum.end2.fastq.gz.end2.fastq.gz --sjdbGTFfile /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Birds/Gallus_gallus-GRCg6a/Gallus_gallus.GRCg6a.102.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 Esophagus-pooled-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/Birds/Gallus_gallus-GRCg6a/STAR --outFileNamePrefix Esophagus-pooled-STAR-2.5.3a/STAR-2.5.3a- --readFilesIn Esophagus.end1.fastq.gz Esophagus.end2.fastq.gz --sjdbGTFfile /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Birds/Gallus_gallus-GRCg6a/Gallus_gallus.GRCg6a.102.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 Gizzard-pooled-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/Birds/Gallus_gallus-GRCg6a/STAR --outFileNamePrefix Gizzard-pooled-STAR-2.5.3a/STAR-2.5.3a- --readFilesIn Gizzard.end1.fastq.gz Gizzard.end2.fastq.gz --sjdbGTFfile /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Birds/Gallus_gallus-GRCg6a/Gallus_gallus.GRCg6a.102.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 Heart-pooled-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/Birds/Gallus_gallus-GRCg6a/STAR --outFileNamePrefix Heart-pooled-STAR-2.5.3a/STAR-2.5.3a- --readFilesIn Heart.end1.fastq.gz Heart.end2.fastq.gz --sjdbGTFfile /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Birds/Gallus_gallus-GRCg6a/Gallus_gallus.GRCg6a.102.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 Hypothalamus-pooled-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/Birds/Gallus_gallus-GRCg6a/STAR --outFileNamePrefix Hypothalamus-pooled-STAR-2.5.3a/STAR-2.5.3a- --readFilesIn Hypothalamus.end1.fastq.gz Hypothalamus.end2.fastq.gz --sjdbGTFfile /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Birds/Gallus_gallus-GRCg6a/Gallus_gallus.GRCg6a.102.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 Ileum-pooled-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/Birds/Gallus_gallus-GRCg6a/STAR --outFileNamePrefix Ileum-pooled-STAR-2.5.3a/STAR-2.5.3a- --readFilesIn Ileum.end1.fastq.gz Ileum.end2.fastq.gz --sjdbGTFfile /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Birds/Gallus_gallus-GRCg6a/Gallus_gallus.GRCg6a.102.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 Jejunum-pooled-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/Birds/Gallus_gallus-GRCg6a/STAR --outFileNamePrefix Jejunum-pooled-STAR-2.5.3a/STAR-2.5.3a- --readFilesIn Jejunum.end1.fastq.gz Jejunum.end2.fastq.gz --sjdbGTFfile /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Birds/Gallus_gallus-GRCg6a/Gallus_gallus.GRCg6a.102.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 Kidney-pooled-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/Birds/Gallus_gallus-GRCg6a/STAR --outFileNamePrefix Kidney-pooled-STAR-2.5.3a/STAR-2.5.3a- --readFilesIn Kidney.end1.fastq.gz Kidney.end2.fastq.gz --sjdbGTFfile /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Birds/Gallus_gallus-GRCg6a/Gallus_gallus.GRCg6a.102.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 Liver-pooled-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/Birds/Gallus_gallus-GRCg6a/STAR --outFileNamePrefix Liver-pooled-STAR-2.5.3a/STAR-2.5.3a- --readFilesIn Liver.end1.fastq.gz Liver.end2.fastq.gz --sjdbGTFfile /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Birds/Gallus_gallus-GRCg6a/Gallus_gallus.GRCg6a.102.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 Lung-pooled-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/Birds/Gallus_gallus-GRCg6a/STAR --outFileNamePrefix Lung-pooled-STAR-2.5.3a/STAR-2.5.3a- --readFilesIn Lung.end1.fastq.gz Lung.end2.fastq.gz --sjdbGTFfile /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Birds/Gallus_gallus-GRCg6a/Gallus_gallus.GRCg6a.102.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 Ovary-pooled-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/Birds/Gallus_gallus-GRCg6a/STAR --outFileNamePrefix Ovary-pooled-STAR-2.5.3a/STAR-2.5.3a- --readFilesIn Ovary.end1.fastq.gz Ovary.end2.fastq.gz --sjdbGTFfile /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Birds/Gallus_gallus-GRCg6a/Gallus_gallus.GRCg6a.102.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 Spleen-pooled-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/Birds/Gallus_gallus-GRCg6a/STAR --outFileNamePrefix Spleen-pooled-STAR-2.5.3a/STAR-2.5.3a- --readFilesIn Spleen.end1.fastq.gz Spleen.end2.fastq.gz --sjdbGTFfile /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Birds/Gallus_gallus-GRCg6a/Gallus_gallus.GRCg6a.102.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 Testis-pooled-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/Birds/Gallus_gallus-GRCg6a/STAR --outFileNamePrefix Testis-pooled-STAR-2.5.3a/STAR-2.5.3a- --readFilesIn Testis.end1.fastq.gz Testis.end2.fastq.gz --sjdbGTFfile /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Birds/Gallus_gallus-GRCg6a/Gallus_gallus.GRCg6a.102.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 Thymus-pooled-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/Birds/Gallus_gallus-GRCg6a/STAR --outFileNamePrefix Thymus-pooled-STAR-2.5.3a/STAR-2.5.3a- --readFilesIn Thymus.end1.fastq.gz Thymus.end2.fastq.gz --sjdbGTFfile /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Birds/Gallus_gallus-GRCg6a/Gallus_gallus.GRCg6a.102.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 Trachea-pooled-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/Birds/Gallus_gallus-GRCg6a/STAR --outFileNamePrefix Trachea-pooled-STAR-2.5.3a/STAR-2.5.3a- --readFilesIn Trachea.end1.fastq.gz Trachea.end2.fastq.gz --sjdbGTFfile /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Birds/Gallus_gallus-GRCg6a/Gallus_gallus.GRCg6a.102.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