Use when aligning RNA-seq reads to a reference genome with splice-aware mapping, generating genome indexes, or performing splice junction detection.
STAR-sse3 --genomeDir /path/to/index --readFilesIn reads.fq/home/vimalinx/miniforge3/envs/bio/bin/STAR-sse3references/help.md for complete options and parameter details# 1) Build a STAR genome index
STAR-sse3 \
--runMode genomeGenerate \
--genomeDir star_index \
--genomeFastaFiles genome.fa \
--sjdbGTFfile genes.gtf \
--runThreadN 16
# 2) Align paired-end gzipped RNA-seq reads
STAR-sse3 \
--genomeDir star_index \
--readFilesIn sample_R1.fastq.gz sample_R2.fastq.gz \
--readFilesCommand zcat \
--runThreadN 16
# 3) Align and emit coordinate-sorted BAM
STAR-sse3 \
--genomeDir star_index \
--readFilesIn sample_R1.fastq.gz sample_R2.fastq.gz \
--readFilesCommand zcat \
--outSAMtype BAM SortedByCoordinate \
--runThreadN 16
--runMode genomeGenerate using FASTA files and optional GTF annotations--runMode alignReads specifying --genomeDir and --readFilesIn--runThreadN to match available CPU cores for parallel processing--runMode genomeGenerate--readFilesCommand (e.g., zcat for .gz files)--genomeSAindexNbases is scaled appropriately for small genomes