/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 SL341_b21_RNA_kidneyreredo.T373_b21_Kidney_PCW15.end1.hg38-STAR-2.5.3a/STAR-2.5.3a --readFilesIn SL341_b21_RNA_kidneyreredo.barcodes_annotated.T373_b21_Kidney_PCW15.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 SL342_b21_RNA_kidneyreredo.T373_b21_Kidney_PCW15.end1.hg38-STAR-2.5.3a/STAR-2.5.3a --readFilesIn SL342_b21_RNA_kidneyreredo.barcodes_annotated.T373_b21_Kidney_PCW15.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 SL341_b21_RNA_kidneyreredo.T397_b21_Kidney_PCW17.end1.hg38-STAR-2.5.3a/STAR-2.5.3a --readFilesIn SL341_b21_RNA_kidneyreredo.barcodes_annotated.T397_b21_Kidney_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 SL342_b21_RNA_kidneyreredo.T397_b21_Kidney_PCW17.end1.hg38-STAR-2.5.3a/STAR-2.5.3a --readFilesIn SL342_b21_RNA_kidneyreredo.barcodes_annotated.T397_b21_Kidney_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 SL341_b21_RNA_kidneyreredo.T42_b21_Kidney_PCW17.end1.hg38-STAR-2.5.3a/STAR-2.5.3a --readFilesIn SL341_b21_RNA_kidneyreredo.barcodes_annotated.T42_b21_Kidney_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 SL342_b21_RNA_kidneyreredo.T42_b21_Kidney_PCW17.end1.hg38-STAR-2.5.3a/STAR-2.5.3a --readFilesIn SL342_b21_RNA_kidneyreredo.barcodes_annotated.T42_b21_Kidney_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 SL341_b21_RNA_kidneyreredo.T228_b21_Kidney_PCW21.end1.hg38-STAR-2.5.3a/STAR-2.5.3a --readFilesIn SL341_b21_RNA_kidneyreredo.barcodes_annotated.T228_b21_Kidney_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 SL342_b21_RNA_kidneyreredo.T228_b21_Kidney_PCW21.end1.hg38-STAR-2.5.3a/STAR-2.5.3a --readFilesIn SL342_b21_RNA_kidneyreredo.barcodes_annotated.T228_b21_Kidney_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 SL341_b21_RNA_kidneyreredo.T271_b21_Kidney_PCW18.end1.hg38-STAR-2.5.3a/STAR-2.5.3a --readFilesIn SL341_b21_RNA_kidneyreredo.barcodes_annotated.T271_b21_Kidney_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 SL342_b21_RNA_kidneyreredo.T271_b21_Kidney_PCW18.end1.hg38-STAR-2.5.3a/STAR-2.5.3a --readFilesIn SL342_b21_RNA_kidneyreredo.barcodes_annotated.T271_b21_Kidney_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 SL341_b21_RNA_kidneyreredo.T108_b21_Kidney_PCW17.end1.hg38-STAR-2.5.3a/STAR-2.5.3a --readFilesIn SL341_b21_RNA_kidneyreredo.barcodes_annotated.T108_b21_Kidney_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 SL342_b21_RNA_kidneyreredo.T108_b21_Kidney_PCW17.end1.hg38-STAR-2.5.3a/STAR-2.5.3a --readFilesIn SL342_b21_RNA_kidneyreredo.barcodes_annotated.T108_b21_Kidney_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 SL277_b10_RNA_StomachEsophagus.T238_b10_Stomach_PCW21.end1.hg38-STAR-2.5.3a/STAR-2.5.3a --readFilesIn SL277_b10_RNA_StomachEsophagus.barcodes_annotated.barcode_T238_b10_Stomach_PCW21.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 SL278_b10_RNA_StomachEsophagus.T238_b10_Stomach_PCW21.end1.hg38-STAR-2.5.3a/STAR-2.5.3a --readFilesIn SL278_b10_RNA_StomachEsophagus.barcodes_annotated.barcode_T238_b10_Stomach_PCW21.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 SL279_b10_RNA_StomachEsophagus.T238_b10_Stomach_PCW21.end1.hg38-STAR-2.5.3a/STAR-2.5.3a --readFilesIn SL279_b10_RNA_StomachEsophagus.barcodes_annotated.barcode_T238_b10_Stomach_PCW21.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 SL280_b10_RNA_StomachEsophagus.T238_b10_Stomach_PCW21.end1.hg38-STAR-2.5.3a/STAR-2.5.3a --readFilesIn SL280_b10_RNA_StomachEsophagus.barcodes_annotated.barcode_T238_b10_Stomach_PCW21.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 SL277_b10_RNA_StomachEsophagus.T269_b10_Stomach_PCW18.end1.hg38-STAR-2.5.3a/STAR-2.5.3a --readFilesIn SL277_b10_RNA_StomachEsophagus.barcodes_annotated.barcode_T269_b10_Stomach_PCW18.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 SL278_b10_RNA_StomachEsophagus.T269_b10_Stomach_PCW18.end1.hg38-STAR-2.5.3a/STAR-2.5.3a --readFilesIn SL278_b10_RNA_StomachEsophagus.barcodes_annotated.barcode_T269_b10_Stomach_PCW18.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 SL279_b10_RNA_StomachEsophagus.T269_b10_Stomach_PCW18.end1.hg38-STAR-2.5.3a/STAR-2.5.3a --readFilesIn SL279_b10_RNA_StomachEsophagus.barcodes_annotated.barcode_T269_b10_Stomach_PCW18.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 SL280_b10_RNA_StomachEsophagus.T269_b10_Stomach_PCW18.end1.hg38-STAR-2.5.3a/STAR-2.5.3a --readFilesIn SL280_b10_RNA_StomachEsophagus.barcodes_annotated.barcode_T269_b10_Stomach_PCW18.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 SL277_b10_RNA_StomachEsophagus.T303_b10_Esophagus_PCW21.end1.hg38-STAR-2.5.3a/STAR-2.5.3a --readFilesIn SL277_b10_RNA_StomachEsophagus.barcodes_annotated.barcode_T303_b10_Esophagus_PCW21.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 SL278_b10_RNA_StomachEsophagus.T303_b10_Esophagus_PCW21.end1.hg38-STAR-2.5.3a/STAR-2.5.3a --readFilesIn SL278_b10_RNA_StomachEsophagus.barcodes_annotated.barcode_T303_b10_Esophagus_PCW21.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 SL279_b10_RNA_StomachEsophagus.T303_b10_Esophagus_PCW21.end1.hg38-STAR-2.5.3a/STAR-2.5.3a --readFilesIn SL279_b10_RNA_StomachEsophagus.barcodes_annotated.barcode_T303_b10_Esophagus_PCW21.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 SL280_b10_RNA_StomachEsophagus.T303_b10_Esophagus_PCW21.end1.hg38-STAR-2.5.3a/STAR-2.5.3a --readFilesIn SL280_b10_RNA_StomachEsophagus.barcodes_annotated.barcode_T303_b10_Esophagus_PCW21.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 SL277_b10_RNA_StomachEsophagus.T322_b10_Stomach_PCW21.end1.hg38-STAR-2.5.3a/STAR-2.5.3a --readFilesIn SL277_b10_RNA_StomachEsophagus.barcodes_annotated.barcode_T322_b10_Stomach_PCW21.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 SL278_b10_RNA_StomachEsophagus.T322_b10_Stomach_PCW21.end1.hg38-STAR-2.5.3a/STAR-2.5.3a --readFilesIn SL278_b10_RNA_StomachEsophagus.barcodes_annotated.barcode_T322_b10_Stomach_PCW21.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 SL279_b10_RNA_StomachEsophagus.T322_b10_Stomach_PCW21.end1.hg38-STAR-2.5.3a/STAR-2.5.3a --readFilesIn SL279_b10_RNA_StomachEsophagus.barcodes_annotated.barcode_T322_b10_Stomach_PCW21.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 SL280_b10_RNA_StomachEsophagus.T322_b10_Stomach_PCW21.end1.hg38-STAR-2.5.3a/STAR-2.5.3a --readFilesIn SL280_b10_RNA_StomachEsophagus.barcodes_annotated.barcode_T322_b10_Stomach_PCW21.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 SL277_b10_RNA_StomachEsophagus.T35_b10_Stomach_PCW17.end1.hg38-STAR-2.5.3a/STAR-2.5.3a --readFilesIn SL277_b10_RNA_StomachEsophagus.barcodes_annotated.barcode_T35_b10_Stomach_PCW17.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 SL278_b10_RNA_StomachEsophagus.T35_b10_Stomach_PCW17.end1.hg38-STAR-2.5.3a/STAR-2.5.3a --readFilesIn SL278_b10_RNA_StomachEsophagus.barcodes_annotated.barcode_T35_b10_Stomach_PCW17.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 SL279_b10_RNA_StomachEsophagus.T35_b10_Stomach_PCW17.end1.hg38-STAR-2.5.3a/STAR-2.5.3a --readFilesIn SL279_b10_RNA_StomachEsophagus.barcodes_annotated.barcode_T35_b10_Stomach_PCW17.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 SL280_b10_RNA_StomachEsophagus.T35_b10_Stomach_PCW17.end1.hg38-STAR-2.5.3a/STAR-2.5.3a --readFilesIn SL280_b10_RNA_StomachEsophagus.barcodes_annotated.barcode_T35_b10_Stomach_PCW17.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 SL277_b10_RNA_StomachEsophagus.T399_b10_Stomach_PCW17.end1.hg38-STAR-2.5.3a/STAR-2.5.3a --readFilesIn SL277_b10_RNA_StomachEsophagus.barcodes_annotated.barcode_T399_b10_Stomach_PCW17.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 SL278_b10_RNA_StomachEsophagus.T399_b10_Stomach_PCW17.end1.hg38-STAR-2.5.3a/STAR-2.5.3a --readFilesIn SL278_b10_RNA_StomachEsophagus.barcodes_annotated.barcode_T399_b10_Stomach_PCW17.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 SL279_b10_RNA_StomachEsophagus.T399_b10_Stomach_PCW17.end1.hg38-STAR-2.5.3a/STAR-2.5.3a --readFilesIn SL279_b10_RNA_StomachEsophagus.barcodes_annotated.barcode_T399_b10_Stomach_PCW17.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 SL280_b10_RNA_StomachEsophagus.T399_b10_Stomach_PCW17.end1.hg38-STAR-2.5.3a/STAR-2.5.3a --readFilesIn SL280_b10_RNA_StomachEsophagus.barcodes_annotated.barcode_T399_b10_Stomach_PCW17.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 SL277_b10_RNA_StomachEsophagus.T53_b10_Stomach_PCW20.end1.hg38-STAR-2.5.3a/STAR-2.5.3a --readFilesIn SL277_b10_RNA_StomachEsophagus.barcodes_annotated.barcode_T53_b10_Stomach_PCW20.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 SL278_b10_RNA_StomachEsophagus.T53_b10_Stomach_PCW20.end1.hg38-STAR-2.5.3a/STAR-2.5.3a --readFilesIn SL278_b10_RNA_StomachEsophagus.barcodes_annotated.barcode_T53_b10_Stomach_PCW20.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 SL279_b10_RNA_StomachEsophagus.T53_b10_Stomach_PCW20.end1.hg38-STAR-2.5.3a/STAR-2.5.3a --readFilesIn SL279_b10_RNA_StomachEsophagus.barcodes_annotated.barcode_T53_b10_Stomach_PCW20.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 SL280_b10_RNA_StomachEsophagus.T53_b10_Stomach_PCW20.end1.hg38-STAR-2.5.3a/STAR-2.5.3a --readFilesIn SL280_b10_RNA_StomachEsophagus.barcodes_annotated.barcode_T53_b10_Stomach_PCW20.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