cd /oak/stanford/groups/akundaje/marinovg/Skin_differentiation_project/2017-05-12-RNA-seq-remap; /oak/stanford/groups/akundaje/marinovg/programs/STAR-2.5.3a/bin/Linux_x86_64_static/STAR --genomeDir /oak/stanford/groups/akundaje/marinovg/genomes/hg19/gencode/gencode_v19/STAR --outFileNamePrefix primary_keratinocyte-d00.RAMPAGE.b1/STAR-2.5.3a --readFilesIn primary_keratinocyte-d00.RAMPAGE.b1.end1.fastq.gz primary_keratinocyte-d00.RAMPAGE.b1.end2.fastq.gz --runThreadN 8 --outSAMunmapped Within --outFilterType BySJout --outSAMattributes NH HI AS NM MD --outFilterMultimapNmax 20 --outSAMstrandField intronMotif --outFilterMismatchNmax 999 --outFilterMismatchNoverReadLmax 0.04 --alignIntronMin 20 --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
cd /oak/stanford/groups/akundaje/marinovg/Skin_differentiation_project/2017-05-12-RNA-seq-remap; /oak/stanford/groups/akundaje/marinovg/programs/STAR-2.5.3a/bin/Linux_x86_64_static/STAR --genomeDir /oak/stanford/groups/akundaje/marinovg/genomes/hg19/gencode/gencode_v19/STAR --outFileNamePrefix primary_keratinocyte-d00.RAMPAGE.b2/STAR-2.5.3a --readFilesIn primary_keratinocyte-d00.RAMPAGE.b2.end1.fastq.gz primary_keratinocyte-d00.RAMPAGE.b2.end2.fastq.gz --runThreadN 8 --outSAMunmapped Within --outFilterType BySJout --outSAMattributes NH HI AS NM MD --outFilterMultimapNmax 20 --outSAMstrandField intronMotif --outFilterMismatchNmax 999 --outFilterMismatchNoverReadLmax 0.04 --alignIntronMin 20 --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
cd /oak/stanford/groups/akundaje/marinovg/Skin_differentiation_project/2017-05-12-RNA-seq-remap; /oak/stanford/groups/akundaje/marinovg/programs/STAR-2.5.3a/bin/Linux_x86_64_static/STAR --genomeDir /oak/stanford/groups/akundaje/marinovg/genomes/hg19/gencode/gencode_v19/STAR --outFileNamePrefix primary_keratinocyte-d05.RAMPAGE.b1/STAR-2.5.3a --readFilesIn primary_keratinocyte-d05.RAMPAGE.b1.end1.fastq.gz primary_keratinocyte-d05.RAMPAGE.b1.end2.fastq.gz --runThreadN 8 --outSAMunmapped Within --outFilterType BySJout --outSAMattributes NH HI AS NM MD --outFilterMultimapNmax 20 --outSAMstrandField intronMotif --outFilterMismatchNmax 999 --outFilterMismatchNoverReadLmax 0.04 --alignIntronMin 20 --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
cd /oak/stanford/groups/akundaje/marinovg/Skin_differentiation_project/2017-05-12-RNA-seq-remap; /oak/stanford/groups/akundaje/marinovg/programs/STAR-2.5.3a/bin/Linux_x86_64_static/STAR --genomeDir /oak/stanford/groups/akundaje/marinovg/genomes/hg19/gencode/gencode_v19/STAR --outFileNamePrefix primary_keratinocyte-d05.RAMPAGE.b2/STAR-2.5.3a --readFilesIn primary_keratinocyte-d05.RAMPAGE.b2.end1.fastq.gz primary_keratinocyte-d05.RAMPAGE.b2.end2.fastq.gz --runThreadN 8 --outSAMunmapped Within --outFilterType BySJout --outSAMattributes NH HI AS NM MD --outFilterMultimapNmax 20 --outSAMstrandField intronMotif --outFilterMismatchNmax 999 --outFilterMismatchNoverReadLmax 0.04 --alignIntronMin 20 --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
cd /oak/stanford/groups/akundaje/marinovg/Skin_differentiation_project/2017-05-12-RNA-seq-remap; /oak/stanford/groups/akundaje/marinovg/programs/STAR-2.5.3a/bin/Linux_x86_64_static/STAR --genomeDir /oak/stanford/groups/akundaje/marinovg/genomes/hg19/gencode/gencode_v19/STAR --outFileNamePrefix primary_keratinocyte-d10.RAMPAGE.b1/STAR-2.5.3a --readFilesIn primary_keratinocyte-d10.RAMPAGE.b1.end1.fastq.gz primary_keratinocyte-d10.RAMPAGE.b1.end2.fastq.gz --runThreadN 8 --outSAMunmapped Within --outFilterType BySJout --outSAMattributes NH HI AS NM MD --outFilterMultimapNmax 20 --outSAMstrandField intronMotif --outFilterMismatchNmax 999 --outFilterMismatchNoverReadLmax 0.04 --alignIntronMin 20 --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
cd /oak/stanford/groups/akundaje/marinovg/Skin_differentiation_project/2017-05-12-RNA-seq-remap; /oak/stanford/groups/akundaje/marinovg/programs/STAR-2.5.3a/bin/Linux_x86_64_static/STAR --genomeDir /oak/stanford/groups/akundaje/marinovg/genomes/hg19/gencode/gencode_v19/STAR --outFileNamePrefix primary_keratinocyte-d10.RAMPAGE.b2/STAR-2.5.3a --readFilesIn primary_keratinocyte-d10.RAMPAGE.b2.end1.fastq.gz primary_keratinocyte-d10.RAMPAGE.b2.end2.fastq.gz --runThreadN 8 --outSAMunmapped Within --outFilterType BySJout --outSAMattributes NH HI AS NM MD --outFilterMultimapNmax 20 --outSAMstrandField intronMotif --outFilterMismatchNmax 999 --outFilterMismatchNoverReadLmax 0.04 --alignIntronMin 20 --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
cd /oak/stanford/groups/akundaje/marinovg/Skin_differentiation_project/2017-05-12-RNA-seq-remap; /oak/stanford/groups/akundaje/marinovg/programs/STAR-2.5.3a/bin/Linux_x86_64_static/STAR --genomeDir /oak/stanford/groups/akundaje/marinovg/genomes/hg19/gencode/gencode_v19/STAR --outFileNamePrefix primary_keratinocyte-d15.RAMPAGE.b1/STAR-2.5.3a --readFilesIn primary_keratinocyte-d15.RAMPAGE.b1.end1.fastq.gz primary_keratinocyte-d15.RAMPAGE.b1.end2.fastq.gz --runThreadN 8 --outSAMunmapped Within --outFilterType BySJout --outSAMattributes NH HI AS NM MD --outFilterMultimapNmax 20 --outSAMstrandField intronMotif --outFilterMismatchNmax 999 --outFilterMismatchNoverReadLmax 0.04 --alignIntronMin 20 --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
cd /oak/stanford/groups/akundaje/marinovg/Skin_differentiation_project/2017-05-12-RNA-seq-remap; /oak/stanford/groups/akundaje/marinovg/programs/STAR-2.5.3a/bin/Linux_x86_64_static/STAR --genomeDir /oak/stanford/groups/akundaje/marinovg/genomes/hg19/gencode/gencode_v19/STAR --outFileNamePrefix primary_keratinocyte-d15.RAMPAGE.b2/STAR-2.5.3a --readFilesIn primary_keratinocyte-d15.RAMPAGE.b2.end1.fastq.gz primary_keratinocyte-d15.RAMPAGE.b2.end2.fastq.gz --runThreadN 8 --outSAMunmapped Within --outFilterType BySJout --outSAMattributes NH HI AS NM MD --outFilterMultimapNmax 20 --outSAMstrandField intronMotif --outFilterMismatchNmax 999 --outFilterMismatchNoverReadLmax 0.04 --alignIntronMin 20 --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