/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/hg20/gencode/gencode_v26/STAR --outFileNamePrefix SL291_b18_RNA_lungredo2.T175_b18_Lung_PCW19.end1.hg38-STAR-2.5.3a/STAR-2.5.3a- --readFilesIn SL291_b18_RNA_lungredo2.barcodes_annotated.T175_b18_Lung_PCW19.RNA_UMI.end1.fastq.gz --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
/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/hg20/gencode/gencode_v26/STAR --outFileNamePrefix SL291_b18_RNA_lungredo2.T198_b18_Lung_PCW23.end1.hg38-STAR-2.5.3a/STAR-2.5.3a- --readFilesIn SL291_b18_RNA_lungredo2.barcodes_annotated.T198_b18_Lung_PCW23.RNA_UMI.end1.fastq.gz --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
/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/hg20/gencode/gencode_v26/STAR --outFileNamePrefix SL291_b18_RNA_lungredo2.T24_b18_Lung_PCW17.end1.hg38-STAR-2.5.3a/STAR-2.5.3a- --readFilesIn SL291_b18_RNA_lungredo2.barcodes_annotated.T24_b18_Lung_PCW17.RNA_UMI.end1.fastq.gz --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
/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/hg20/gencode/gencode_v26/STAR --outFileNamePrefix SL291_b18_RNA_lungredo2.T305_b18_Lung_PCW21.end1.hg38-STAR-2.5.3a/STAR-2.5.3a- --readFilesIn SL291_b18_RNA_lungredo2.barcodes_annotated.T305_b18_Lung_PCW21.RNA_UMI.end1.fastq.gz --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
/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/hg20/gencode/gencode_v26/STAR --outFileNamePrefix SL291_b18_RNA_lungredo2.T333_b18_Lung_PCW21.end1.hg38-STAR-2.5.3a/STAR-2.5.3a- --readFilesIn SL291_b18_RNA_lungredo2.barcodes_annotated.T333_b18_Lung_PCW21.RNA_UMI.end1.fastq.gz --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
/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/hg20/gencode/gencode_v26/STAR --outFileNamePrefix SL291_b18_RNA_lungredo2.T49_b18_Lung_PCW20.end1.hg38-STAR-2.5.3a/STAR-2.5.3a- --readFilesIn SL291_b18_RNA_lungredo2.barcodes_annotated.T49_b18_Lung_PCW20.RNA_UMI.end1.fastq.gz --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
/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/hg20/gencode/gencode_v26/STAR --outFileNamePrefix SL291_b18_RNA_lungredo2.T77_b18_Lung_PCW18.end1.hg38-STAR-2.5.3a/STAR-2.5.3a- --readFilesIn SL291_b18_RNA_lungredo2.barcodes_annotated.T77_b18_Lung_PCW18.RNA_UMI.end1.fastq.gz --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
/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/hg20/gencode/gencode_v26/STAR --outFileNamePrefix SL292_b18_RNA_lungredo2.T175_b18_Lung_PCW19.end1.hg38-STAR-2.5.3a/STAR-2.5.3a- --readFilesIn SL292_b18_RNA_lungredo2.barcodes_annotated.T175_b18_Lung_PCW19.RNA_UMI.end1.fastq.gz --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
/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/hg20/gencode/gencode_v26/STAR --outFileNamePrefix SL292_b18_RNA_lungredo2.T198_b18_Lung_PCW23.end1.hg38-STAR-2.5.3a/STAR-2.5.3a- --readFilesIn SL292_b18_RNA_lungredo2.barcodes_annotated.T198_b18_Lung_PCW23.RNA_UMI.end1.fastq.gz --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
/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/hg20/gencode/gencode_v26/STAR --outFileNamePrefix SL292_b18_RNA_lungredo2.T24_b18_Lung_PCW17.end1.hg38-STAR-2.5.3a/STAR-2.5.3a- --readFilesIn SL292_b18_RNA_lungredo2.barcodes_annotated.T24_b18_Lung_PCW17.RNA_UMI.end1.fastq.gz --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
/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/hg20/gencode/gencode_v26/STAR --outFileNamePrefix SL292_b18_RNA_lungredo2.T305_b18_Lung_PCW21.end1.hg38-STAR-2.5.3a/STAR-2.5.3a- --readFilesIn SL292_b18_RNA_lungredo2.barcodes_annotated.T305_b18_Lung_PCW21.RNA_UMI.end1.fastq.gz --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
/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/hg20/gencode/gencode_v26/STAR --outFileNamePrefix SL292_b18_RNA_lungredo2.T333_b18_Lung_PCW21.end1.hg38-STAR-2.5.3a/STAR-2.5.3a- --readFilesIn SL292_b18_RNA_lungredo2.barcodes_annotated.T333_b18_Lung_PCW21.RNA_UMI.end1.fastq.gz --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
/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/hg20/gencode/gencode_v26/STAR --outFileNamePrefix SL292_b18_RNA_lungredo2.T49_b18_Lung_PCW20.end1.hg38-STAR-2.5.3a/STAR-2.5.3a- --readFilesIn SL292_b18_RNA_lungredo2.barcodes_annotated.T49_b18_Lung_PCW20.RNA_UMI.end1.fastq.gz --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
/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/hg20/gencode/gencode_v26/STAR --outFileNamePrefix SL292_b18_RNA_lungredo2.T77_b18_Lung_PCW18.end1.hg38-STAR-2.5.3a/STAR-2.5.3a- --readFilesIn SL292_b18_RNA_lungredo2.barcodes_annotated.T77_b18_Lung_PCW18.RNA_UMI.end1.fastq.gz --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
/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/hg20/gencode/gencode_v26/STAR --outFileNamePrefix SL294_b18_RNA_lungredo2.T175_b18_Lung_PCW19.end1.hg38-STAR-2.5.3a/STAR-2.5.3a- --readFilesIn SL294_b18_RNA_lungredo2.barcodes_annotated.T175_b18_Lung_PCW19.RNA_UMI.end1.fastq.gz --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
/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/hg20/gencode/gencode_v26/STAR --outFileNamePrefix SL294_b18_RNA_lungredo2.T198_b18_Lung_PCW23.end1.hg38-STAR-2.5.3a/STAR-2.5.3a- --readFilesIn SL294_b18_RNA_lungredo2.barcodes_annotated.T198_b18_Lung_PCW23.RNA_UMI.end1.fastq.gz --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
/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/hg20/gencode/gencode_v26/STAR --outFileNamePrefix SL294_b18_RNA_lungredo2.T24_b18_Lung_PCW17.end1.hg38-STAR-2.5.3a/STAR-2.5.3a- --readFilesIn SL294_b18_RNA_lungredo2.barcodes_annotated.T24_b18_Lung_PCW17.RNA_UMI.end1.fastq.gz --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
/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/hg20/gencode/gencode_v26/STAR --outFileNamePrefix SL294_b18_RNA_lungredo2.T305_b18_Lung_PCW21.end1.hg38-STAR-2.5.3a/STAR-2.5.3a- --readFilesIn SL294_b18_RNA_lungredo2.barcodes_annotated.T305_b18_Lung_PCW21.RNA_UMI.end1.fastq.gz --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
/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/hg20/gencode/gencode_v26/STAR --outFileNamePrefix SL294_b18_RNA_lungredo2.T333_b18_Lung_PCW21.end1.hg38-STAR-2.5.3a/STAR-2.5.3a- --readFilesIn SL294_b18_RNA_lungredo2.barcodes_annotated.T333_b18_Lung_PCW21.RNA_UMI.end1.fastq.gz --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
/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/hg20/gencode/gencode_v26/STAR --outFileNamePrefix SL294_b18_RNA_lungredo2.T49_b18_Lung_PCW20.end1.hg38-STAR-2.5.3a/STAR-2.5.3a- --readFilesIn SL294_b18_RNA_lungredo2.barcodes_annotated.T49_b18_Lung_PCW20.RNA_UMI.end1.fastq.gz --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
/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/hg20/gencode/gencode_v26/STAR --outFileNamePrefix SL294_b18_RNA_lungredo2.T77_b18_Lung_PCW18.end1.hg38-STAR-2.5.3a/STAR-2.5.3a- --readFilesIn SL294_b18_RNA_lungredo2.barcodes_annotated.T77_b18_Lung_PCW18.RNA_UMI.end1.fastq.gz --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
/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/hg20/gencode/gencode_v26/STAR --outFileNamePrefix SL293_b18_RNA_lungredo2.T175_b18_Lung_PCW19.end1.hg38-STAR-2.5.3a/STAR-2.5.3a- --readFilesIn SL293_b18_RNA_lungredo2.barcodes_annotated.T175_b18_Lung_PCW19.RNA_UMI.end1.fastq.gz --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
/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/hg20/gencode/gencode_v26/STAR --outFileNamePrefix SL293_b18_RNA_lungredo2.T198_b18_Lung_PCW23.end1.hg38-STAR-2.5.3a/STAR-2.5.3a- --readFilesIn SL293_b18_RNA_lungredo2.barcodes_annotated.T198_b18_Lung_PCW23.RNA_UMI.end1.fastq.gz --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
/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/hg20/gencode/gencode_v26/STAR --outFileNamePrefix SL293_b18_RNA_lungredo2.T24_b18_Lung_PCW17.end1.hg38-STAR-2.5.3a/STAR-2.5.3a- --readFilesIn SL293_b18_RNA_lungredo2.barcodes_annotated.T24_b18_Lung_PCW17.RNA_UMI.end1.fastq.gz --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
/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/hg20/gencode/gencode_v26/STAR --outFileNamePrefix SL293_b18_RNA_lungredo2.T305_b18_Lung_PCW21.end1.hg38-STAR-2.5.3a/STAR-2.5.3a- --readFilesIn SL293_b18_RNA_lungredo2.barcodes_annotated.T305_b18_Lung_PCW21.RNA_UMI.end1.fastq.gz --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
/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/hg20/gencode/gencode_v26/STAR --outFileNamePrefix SL293_b18_RNA_lungredo2.T333_b18_Lung_PCW21.end1.hg38-STAR-2.5.3a/STAR-2.5.3a- --readFilesIn SL293_b18_RNA_lungredo2.barcodes_annotated.T333_b18_Lung_PCW21.RNA_UMI.end1.fastq.gz --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
/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/hg20/gencode/gencode_v26/STAR --outFileNamePrefix SL293_b18_RNA_lungredo2.T49_b18_Lung_PCW20.end1.hg38-STAR-2.5.3a/STAR-2.5.3a- --readFilesIn SL293_b18_RNA_lungredo2.barcodes_annotated.T49_b18_Lung_PCW20.RNA_UMI.end1.fastq.gz --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
/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/hg20/gencode/gencode_v26/STAR --outFileNamePrefix SL293_b18_RNA_lungredo2.T77_b18_Lung_PCW18.end1.hg38-STAR-2.5.3a/STAR-2.5.3a- --readFilesIn SL293_b18_RNA_lungredo2.barcodes_annotated.T77_b18_Lung_PCW18.RNA_UMI.end1.fastq.gz --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
/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/hg20/gencode/gencode_v26/STAR --outFileNamePrefix SL295_b18_RNA_lungredo2.T175_b18_Lung_PCW19.end1.hg38-STAR-2.5.3a/STAR-2.5.3a- --readFilesIn SL295_b18_RNA_lungredo2.barcodes_annotated.T175_b18_Lung_PCW19.RNA_UMI.end1.fastq.gz --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
/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/hg20/gencode/gencode_v26/STAR --outFileNamePrefix SL295_b18_RNA_lungredo2.T198_b18_Lung_PCW23.end1.hg38-STAR-2.5.3a/STAR-2.5.3a- --readFilesIn SL295_b18_RNA_lungredo2.barcodes_annotated.T198_b18_Lung_PCW23.RNA_UMI.end1.fastq.gz --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
/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/hg20/gencode/gencode_v26/STAR --outFileNamePrefix SL295_b18_RNA_lungredo2.T24_b18_Lung_PCW17.end1.hg38-STAR-2.5.3a/STAR-2.5.3a- --readFilesIn SL295_b18_RNA_lungredo2.barcodes_annotated.T24_b18_Lung_PCW17.RNA_UMI.end1.fastq.gz --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
/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/hg20/gencode/gencode_v26/STAR --outFileNamePrefix SL295_b18_RNA_lungredo2.T305_b18_Lung_PCW21.end1.hg38-STAR-2.5.3a/STAR-2.5.3a- --readFilesIn SL295_b18_RNA_lungredo2.barcodes_annotated.T305_b18_Lung_PCW21.RNA_UMI.end1.fastq.gz --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
/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/hg20/gencode/gencode_v26/STAR --outFileNamePrefix SL295_b18_RNA_lungredo2.T333_b18_Lung_PCW21.end1.hg38-STAR-2.5.3a/STAR-2.5.3a- --readFilesIn SL295_b18_RNA_lungredo2.barcodes_annotated.T333_b18_Lung_PCW21.RNA_UMI.end1.fastq.gz --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
/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/hg20/gencode/gencode_v26/STAR --outFileNamePrefix SL295_b18_RNA_lungredo2.T49_b18_Lung_PCW20.end1.hg38-STAR-2.5.3a/STAR-2.5.3a- --readFilesIn SL295_b18_RNA_lungredo2.barcodes_annotated.T49_b18_Lung_PCW20.RNA_UMI.end1.fastq.gz --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
/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/hg20/gencode/gencode_v26/STAR --outFileNamePrefix SL295_b18_RNA_lungredo2.T77_b18_Lung_PCW18.end1.hg38-STAR-2.5.3a/STAR-2.5.3a- --readFilesIn SL295_b18_RNA_lungredo2.barcodes_annotated.T77_b18_Lung_PCW18.RNA_UMI.end1.fastq.gz --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
/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/hg20/gencode/gencode_v26/STAR --outFileNamePrefix SL296_b18_RNA_lungredo2.T175_b18_Lung_PCW19.end1.hg38-STAR-2.5.3a/STAR-2.5.3a- --readFilesIn SL296_b18_RNA_lungredo2.barcodes_annotated.T175_b18_Lung_PCW19.RNA_UMI.end1.fastq.gz --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
/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/hg20/gencode/gencode_v26/STAR --outFileNamePrefix SL296_b18_RNA_lungredo2.T198_b18_Lung_PCW23.end1.hg38-STAR-2.5.3a/STAR-2.5.3a- --readFilesIn SL296_b18_RNA_lungredo2.barcodes_annotated.T198_b18_Lung_PCW23.RNA_UMI.end1.fastq.gz --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
/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/hg20/gencode/gencode_v26/STAR --outFileNamePrefix SL296_b18_RNA_lungredo2.T24_b18_Lung_PCW17.end1.hg38-STAR-2.5.3a/STAR-2.5.3a- --readFilesIn SL296_b18_RNA_lungredo2.barcodes_annotated.T24_b18_Lung_PCW17.RNA_UMI.end1.fastq.gz --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
/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/hg20/gencode/gencode_v26/STAR --outFileNamePrefix SL296_b18_RNA_lungredo2.T305_b18_Lung_PCW21.end1.hg38-STAR-2.5.3a/STAR-2.5.3a- --readFilesIn SL296_b18_RNA_lungredo2.barcodes_annotated.T305_b18_Lung_PCW21.RNA_UMI.end1.fastq.gz --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
/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/hg20/gencode/gencode_v26/STAR --outFileNamePrefix SL296_b18_RNA_lungredo2.T333_b18_Lung_PCW21.end1.hg38-STAR-2.5.3a/STAR-2.5.3a- --readFilesIn SL296_b18_RNA_lungredo2.barcodes_annotated.T333_b18_Lung_PCW21.RNA_UMI.end1.fastq.gz --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
/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/hg20/gencode/gencode_v26/STAR --outFileNamePrefix SL296_b18_RNA_lungredo2.T49_b18_Lung_PCW20.end1.hg38-STAR-2.5.3a/STAR-2.5.3a- --readFilesIn SL296_b18_RNA_lungredo2.barcodes_annotated.T49_b18_Lung_PCW20.RNA_UMI.end1.fastq.gz --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
/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/hg20/gencode/gencode_v26/STAR --outFileNamePrefix SL296_b18_RNA_lungredo2.T77_b18_Lung_PCW18.end1.hg38-STAR-2.5.3a/STAR-2.5.3a- --readFilesIn SL296_b18_RNA_lungredo2.barcodes_annotated.T77_b18_Lung_PCW18.RNA_UMI.end1.fastq.gz --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