Use when aligning spliced RNA-seq reads to a reference genome, generating genome indices, or performing splice-aware alignment for transcriptome analysis.
STAR/home/vimalinx/miniforge3/envs/bio/bin/STARreferences/help.mdSJ.out.tab and alignment QC from Log.final.out.STAR over subread-align when intron-spanning alignment is the main job.# 1) Build a STAR genome index once per reference/annotation pair
STAR \
--runMode genomeGenerate \
--runThreadN 16 \
--genomeDir star_index \
--genomeFastaFiles genome.fa \
--sjdbGTFfile genes.gtf \
--sjdbOverhang 149
# 2) Align paired-end gzipped RNA-seq reads and emit sorted BAM
STAR \
--runThreadN 16 \
--genomeDir star_index \
--readFilesIn sample_R1.fastq.gz sample_R2.fastq.gz \
--readFilesCommand zcat \
--outSAMtype BAM SortedByCoordinate \
--outFileNamePrefix sample.
# 3) Add simple gene-level quantification during alignment
STAR \
--runThreadN 16 \
--genomeDir star_index \
--readFilesIn sample_R1.fastq.gz sample_R2.fastq.gz \
--readFilesCommand zcat \
--outSAMtype BAM SortedByCoordinate \
--quantMode GeneCounts \
--outFileNamePrefix sample.
--genomeDir, --readFilesIn, and --readFilesCommand zcat for gzipped FASTQ.Log.final.out, SJ.out.tab, and BAM size before moving into counting.featureCounts or another quantifier using the same annotation build.--genomeFastaFiles for genome generation must be plain-text FASTA, not gzipped FASTA.--sjdbOverhang to read length minus 1 for the library you are aligning.--genomeSAindexNbases as documented in references/help.md.