/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	BMMC_single_donor_RNA.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-	--readFilesIn	BMMC_single_donor_RNA.barcodes_annotated.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