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/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 SL228_b15_RNA_LiverRedo.T166_b15_Liver_PCW19.end1.hg38-STAR-2.5.3a/STAR-2.5.3a- --readFilesIn SL228_b15_RNA_LiverRedo.barcodes_annotated.RNA_UMI.barcode_T166_b15_Liver_PCW19.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