/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 13004_1_CTCFvalidationRNAseq_170812_S9-2x50mers-STAR2.5.3a-GENCODEV19/STAR-2.5.3a- --readFilesIn 13004_1_CTCFvalidationRNAseq_170812_S9.50mers.end1.fastq.gz 13004_1_CTCFvalidationRNAseq_170812_S9.50mers.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
/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 13004_2_CTCFvalidationRNAseq_170812_S10-2x50mers-STAR2.5.3a-GENCODEV19/STAR-2.5.3a- --readFilesIn 13004_2_CTCFvalidationRNAseq_170812_S10.50mers.end1.fastq.gz 13004_2_CTCFvalidationRNAseq_170812_S10.50mers.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
/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 13006_1_CTCFvalidationRNAseq_170812_S11-2x50mers-STAR2.5.3a-GENCODEV19/STAR-2.5.3a- --readFilesIn 13006_1_CTCFvalidationRNAseq_170812_S11.50mers.end1.fastq.gz 13006_1_CTCFvalidationRNAseq_170812_S11.50mers.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
/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 13006_2_CTCFvalidationRNAseq_170812_S12-2x50mers-STAR2.5.3a-GENCODEV19/STAR-2.5.3a- --readFilesIn 13006_2_CTCFvalidationRNAseq_170812_S12.50mers.end1.fastq.gz 13006_2_CTCFvalidationRNAseq_170812_S12.50mers.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
/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 12040-GH549_1_CTCFvalidationRNAseq_170812_S1-2x50mers-STAR2.5.3a-GENCODEV19/STAR-2.5.3a- --readFilesIn 12040-GH549_1_CTCFvalidationRNAseq_170812_S1.50mers.end1.fastq.gz 12040-GH549_1_CTCFvalidationRNAseq_170812_S1.50mers.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
/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 12040-GH549_2_CTCFvalidationRNAseq_170812_S2-2x50mers-STAR2.5.3a-GENCODEV19/STAR-2.5.3a- --readFilesIn 12040-GH549_2_CTCFvalidationRNAseq_170812_S2.50mers.end1.fastq.gz 12040-GH549_2_CTCFvalidationRNAseq_170812_S2.50mers.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
/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 12042-GH550_1_CTCFvalidationRNAseq_170812_S3-2x50mers-STAR2.5.3a-GENCODEV19/STAR-2.5.3a- --readFilesIn 12042-GH550_1_CTCFvalidationRNAseq_170812_S3.50mers.end1.fastq.gz 12042-GH550_1_CTCFvalidationRNAseq_170812_S3.50mers.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
/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 12042-GH550_2_CTCFvalidationRNAseq_170812_S4-2x50mers-STAR2.5.3a-GENCODEV19/STAR-2.5.3a- --readFilesIn 12042-GH550_2_CTCFvalidationRNAseq_170812_S4.50mers.end1.fastq.gz 12042-GH550_2_CTCFvalidationRNAseq_170812_S4.50mers.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
/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 14376-GH551_1_CTCFvalidationRNAseq_170812_S5-2x50mers-STAR2.5.3a-GENCODEV19/STAR-2.5.3a- --readFilesIn 14376-GH551_1_CTCFvalidationRNAseq_170812_S5.50mers.end1.fastq.gz 14376-GH551_1_CTCFvalidationRNAseq_170812_S5.50mers.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
/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 14376-GH551_2_CTCFvalidationRNAseq_170812_S6-2x50mers-STAR2.5.3a-GENCODEV19/STAR-2.5.3a- --readFilesIn 14376-GH551_2_CTCFvalidationRNAseq_170812_S6.50mers.end1.fastq.gz 14376-GH551_2_CTCFvalidationRNAseq_170812_S6.50mers.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
/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 14377-GH552_1_CTCFvalidationRNAseq_170812_S7-2x50mers-STAR2.5.3a-GENCODEV19/STAR-2.5.3a- --readFilesIn 14377-GH552_1_CTCFvalidationRNAseq_170812_S7.50mers.end1.fastq.gz 14377-GH552_1_CTCFvalidationRNAseq_170812_S7.50mers.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
/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 14377-GH552_2_CTCFvalidationRNAseq_170812_S8-2x50mers-STAR2.5.3a-GENCODEV19/STAR-2.5.3a- --readFilesIn 14377-GH552_2_CTCFvalidationRNAseq_170812_S8.50mers.end1.fastq.gz 14377-GH552_2_CTCFvalidationRNAseq_170812_S8.50mers.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
/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 N4293_1_CTCFvalidationRNAseq_170812_S13-2x50mers-STAR2.5.3a-GENCODEV19/STAR-2.5.3a- --readFilesIn N4293_1_CTCFvalidationRNAseq_170812_S13.50mers.end1.fastq.gz N4293_1_CTCFvalidationRNAseq_170812_S13.50mers.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
/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 N4293_2_CTCFvalidationRNAseq_170812_S14-2x50mers-STAR2.5.3a-GENCODEV19/STAR-2.5.3a- --readFilesIn N4293_2_CTCFvalidationRNAseq_170812_S14.50mers.end1.fastq.gz N4293_2_CTCFvalidationRNAseq_170812_S14.50mers.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
/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 N4871_1_CTCFvalidationRNAseq_170812_S15-2x50mers-STAR2.5.3a-GENCODEV19/STAR-2.5.3a- --readFilesIn N4871_1_CTCFvalidationRNAseq_170812_S15.50mers.end1.fastq.gz N4871_1_CTCFvalidationRNAseq_170812_S15.50mers.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
/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 N4871_2_CTCFvalidationRNAseq_170812_S16-2x50mers-STAR2.5.3a-GENCODEV19/STAR-2.5.3a- --readFilesIn N4871_2_CTCFvalidationRNAseq_170812_S16.50mers.end1.fastq.gz N4871_2_CTCFvalidationRNAseq_170812_S16.50mers.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
