Use when aligning RNA-seq reads to a reference genome with splice-aware mapping, generating genome indices, or performing related operations like lift-over and BAM input processing.
STAR-plain/home/vimalinx/miniforge3/envs/bio/bin/STAR-plainreferences/help.md# 1) Build a STAR genome index
STAR-plain \
--runMode genomeGenerate \
--genomeDir star_index \
--genomeFastaFiles genome.fa \
--sjdbGTFfile genes.gtf \
--runThreadN 16
# 2) Align paired-end gzipped RNA-seq reads
STAR-plain \
--genomeDir star_index \
--readFilesIn sample_R1.fastq.gz sample_R2.fastq.gz \
--readFilesCommand zcat \
--runThreadN 16
# 3) Align and emit coordinate-sorted BAM
STAR-plain \
--genomeDir star_index \
--readFilesIn sample_R1.fastq.gz sample_R2.fastq.gz \
--readFilesCommand zcat \
--outSAMtype BAM SortedByCoordinate \
--runThreadN 16
STAR-plain --runMode genomeGenerate --genomeDir /path/to/index --genomeFastaFiles genome.fa --sjdbGTFfile annotations.gtf --runThreadN NSTAR-plain --genomeDir /path/to/index --readFilesIn R1.fq R2.fq --runThreadN N--readFilesCommand zcat for .gz files or bzcat for .bz2 filesSJ.out.tab--genomeSAindexNbases down for small genomes: use min(14, log2(GenomeLength)/2 - 1)--genomeLoad NoSharedMemory for isolated runs to avoid shared memory issues on some systems--readFilesCommand zcat