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.PAS-seq.b1/STAR-2.5.3a --readFilesIn primary_keratinocyte-d00.GGR.Stanford_Khavari.PAS-seq.b1.t1.GGTGAG.1.fastq.gz primary_keratinocyte-d00.GGR.Stanford_Khavari.PAS-seq.b1.t1.GGTGAG.2.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.PAS-seq.b2/STAR-2.5.3a --readFilesIn primary_keratinocyte-d00.GGR.Stanford_Khavari.PAS-seq.b2.t1.GCGAAT.1.fastq.gz primary_keratinocyte-d00.GGR.Stanford_Khavari.PAS-seq.b2.t1.GCGAAT.2.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.PAS-seq.b1/STAR-2.5.3a --readFilesIn primary_keratinocyte-d05.GGR.Stanford_Khavari.PAS-seq.b1.t1.CGGTTA.1.fastq.gz primary_keratinocyte-d05.GGR.Stanford_Khavari.PAS-seq.b1.t1.CGGTTA.2.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.PAS-seq.b2/STAR-2.5.3a --readFilesIn primary_keratinocyte-d05.GGR.Stanford_Khavari.PAS-seq.b2.t1.TGGCGA.1.fastq.gz primary_keratinocyte-d05.GGR.Stanford_Khavari.PAS-seq.b2.t1.TGGCGA.2.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.PAS-seq.b1/STAR-2.5.3a --readFilesIn primary_keratinocyte-d10.GGR.Stanford_Khavari.PAS-seq.b1.t1.GCGCTG.1.fastq.gz primary_keratinocyte-d10.GGR.Stanford_Khavari.PAS-seq.b1.t1.GCGCTG.2.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.PAS-seq.b2/STAR-2.5.3a --readFilesIn primary_keratinocyte-d10.GGR.Stanford_Khavari.PAS-seq.b2.t1.CAATGC.1.fastq.gz primary_keratinocyte-d10.GGR.Stanford_Khavari.PAS-seq.b2.t1.CAATGC.2.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.PAS-seq.b1/STAR-2.5.3a --readFilesIn primary_keratinocyte-d15.GGR.Stanford_Khavari.PAS-seq.b1.t1.GACGAT.1.fastq.gz primary_keratinocyte-d15.GGR.Stanford_Khavari.PAS-seq.b1.t1.GACGAT.2.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.PAS-seq.b2/STAR-2.5.3a --readFilesIn primary_keratinocyte-d15.GGR.Stanford_Khavari.PAS-seq.b2.t1.AAGACA.1.fastq.gz primary_keratinocyte-d15.GGR.Stanford_Khavari.PAS-seq.b2.t1.AAGACA.2.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-d20.PAS-seq.b1/STAR-2.5.3a --readFilesIn primary_keratinocyte-d20.GGR.Stanford_Khavari.PAS-seq.b1.t1.ACCTAC.1.fastq.gz primary_keratinocyte-d20.GGR.Stanford_Khavari.PAS-seq.b1.t1.ACCTAC.2.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-d20.PAS-seq.b2/STAR-2.5.3a --readFilesIn primary_keratinocyte-d20.GGR.Stanford_Khavari.PAS-seq.b2.t1.CAGATG.1.fastq.gz primary_keratinocyte-d20.GGR.Stanford_Khavari.PAS-seq.b2.t1.CAGATG.2.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-d25.PAS-seq.b1/STAR-2.5.3a --readFilesIn primary_keratinocyte-d25.GGR.Stanford_Khavari.PAS-seq.b1.t1.AGAATC.1.fastq.gz primary_keratinocyte-d25.GGR.Stanford_Khavari.PAS-seq.b1.t1.AGAATC.2.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-d25.PAS-seq.b2/STAR-2.5.3a --readFilesIn primary_keratinocyte-d25.GGR.Stanford_Khavari.PAS-seq.b2.t1.GTTACC.1.fastq.gz primary_keratinocyte-d25.GGR.Stanford_Khavari.PAS-seq.b2.t1.GTTACC.2.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-d30.PAS-seq.b1/STAR-2.5.3a --readFilesIn primary_keratinocyte-d30.GGR.Stanford_Khavari.PAS-seq.b1.t1.AACCGA.1.fastq.gz primary_keratinocyte-d30.GGR.Stanford_Khavari.PAS-seq.b1.t1.AACCGA.2.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-d30.PAS-seq.b2/STAR-2.5.3a --readFilesIn primary_keratinocyte-d30.GGR.Stanford_Khavari.PAS-seq.b2.t1.CAGCGT.1.fastq.gz primary_keratinocyte-d30.GGR.Stanford_Khavari.PAS-seq.b2.t1.CAGCGT.2.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-d35.PAS-seq.b1/STAR-2.5.3a --readFilesIn primary_keratinocyte-d35.GGR.Stanford_Khavari.PAS-seq.b1.t1.CAACAG.1.fastq.gz primary_keratinocyte-d35.GGR.Stanford_Khavari.PAS-seq.b1.t1.CAACAG.2.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-d35.PAS-seq.b2/STAR-2.5.3a --readFilesIn primary_keratinocyte-d35.GGR.Stanford_Khavari.PAS-seq.b2.t1.GCAGCC.1.fastq.gz primary_keratinocyte-d35.GGR.Stanford_Khavari.PAS-seq.b2.t1.GCAGCC.2.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-d40.PAS-seq.b1/STAR-2.5.3a --readFilesIn primary_keratinocyte-d40.GGR.Stanford_Khavari.PAS-seq.b1.t1.CGAAGG.1.fastq.gz primary_keratinocyte-d40.GGR.Stanford_Khavari.PAS-seq.b1.t1.CGAAGG.2.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-d40.PAS-seq.b2/STAR-2.5.3a --readFilesIn primary_keratinocyte-d40.GGR.Stanford_Khavari.PAS-seq.b2.t1.CGATCT.1.fastq.gz primary_keratinocyte-d40.GGR.Stanford_Khavari.PAS-seq.b2.t1.CGATCT.2.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-d45.PAS-seq.b1/STAR-2.5.3a --readFilesIn primary_keratinocyte-d45.GGR.Stanford_Khavari.PAS-seq.b1.t1.AACGCC.1.fastq.gz primary_keratinocyte-d45.GGR.Stanford_Khavari.PAS-seq.b1.t1.AACGCC.2.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-d45.PAS-seq.b2/STAR-2.5.3a --readFilesIn primary_keratinocyte-d45.GGR.Stanford_Khavari.PAS-seq.b2.t1.CACTAA.1.fastq.gz primary_keratinocyte-d45.GGR.Stanford_Khavari.PAS-seq.b2.t1.CACTAA.2.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-d50.PAS-seq.b1/STAR-2.5.3a --readFilesIn primary_keratinocyte-d50.GGR.Stanford_Khavari.PAS-seq.b1.t1.CAAGCA.1.fastq.gz primary_keratinocyte-d50.GGR.Stanford_Khavari.PAS-seq.b1.t1.CAAGCA.2.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-d50.PAS-seq.b2/STAR-2.5.3a --readFilesIn primary_keratinocyte-d50.GGR.Stanford_Khavari.PAS-seq.b2.t1.GGAGGT.1.fastq.gz primary_keratinocyte-d50.GGR.Stanford_Khavari.PAS-seq.b2.t1.GGAGGT.2.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-d55.PAS-seq.b1/STAR-2.5.3a --readFilesIn primary_keratinocyte-d55.GGR.Stanford_Khavari.PAS-seq.b1.t1.CACACT.1.fastq.gz primary_keratinocyte-d55.GGR.Stanford_Khavari.PAS-seq.b1.t1.CACACT.2.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-d55.PAS-seq.b2/STAR-2.5.3a --readFilesIn primary_keratinocyte-d55.GGR.Stanford_Khavari.PAS-seq.b2.t1.TAATCG.1.fastq.gz primary_keratinocyte-d55.GGR.Stanford_Khavari.PAS-seq.b2.t1.TAATCG.2.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-d60.PAS-seq.b1/STAR-2.5.3a --readFilesIn primary_keratinocyte-d60.GGR.Stanford_Khavari.PAS-seq.b1.t1.TGGATT.1.fastq.gz primary_keratinocyte-d60.GGR.Stanford_Khavari.PAS-seq.b1.t1.TGGATT.2.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-d60.PAS-seq.b2/STAR-2.5.3a --readFilesIn primary_keratinocyte-d60.GGR.Stanford_Khavari.PAS-seq.b2.t1.GATCAC.1.fastq.gz primary_keratinocyte-d60.GGR.Stanford_Khavari.PAS-seq.b2.t1.GATCAC.2.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