# Index building

STAR --runThreadN 5 \

--runMode genomeGenerate \

--genomeDir STAR_100_index \

--genomeFastaFiles GRCm38.primary_assembly.genome.fa \

--sjdbGTFfile gencode.vM10.annotation.gtf \

--sjdbOverhang 100

# Example run for single-end cell

/data/yosef2/users/cfbuenabadn/software/STAR-2.5.3a/bin/Linux_x86_64/STAR --runThreadN 4 \

--genomeDir /data/yosef2/users/cfbuenabadn/mm10/STAR_100_index \

--readFilesIn SRR2727450.fastq \ # a second fastq file is listed for paired-end datasets

--quantMode GeneCounts \

--twopassMode Basic \

--outFileNamePrefix /data/yosef2/scratch/cfbuenabadn/ChenRNASeq/SRR2727450/star_output/ \

--outSAMstrandField intronMotif \

--outSAMtype BAM SortedByCoordinate \

--outReadsUnmapped Fastx

Note: STAR performs soft-trimming of reads (Doubin et al, 2013). Therefore, we do not run trimmomatic before mapping.