Use when aligning long RNA-seq reads to a reference genome using STARlong with SSE3 optimization, or when generating genome indices for long-read splice-aware alignment.
STARlong-sse3/home/vimalinx/miniforge3/envs/bio/bin/STARlong-sse3# 1) Build a genome index for STARlong
STARlong-sse3 \
--runMode genomeGenerate \
--genomeDir starlong_index \
--genomeFastaFiles genome.fa \
--sjdbGTFfile genes.gtf \
--runThreadN 16
# 2) Align long reads from FASTQ
STARlong-sse3 \
--genomeDir starlong_index \
--readFilesIn longreads.fastq \
--runThreadN 16
# 3) Align gzipped long reads and emit sorted BAM
STARlong-sse3 \
--genomeDir starlong_index \
--readFilesIn longreads.fastq.gz \
--readFilesCommand zcat \
--outSAMtype BAM SortedByCoordinate \
--runThreadN 16
--sjdbGTFfile for splice junction annotation.--runMode genomeGenerate --genomeDir <dir> --genomeFastaFiles <fasta>.--runMode alignReads --genomeDir <dir> --readFilesIn <reads.fq>.--genomeDir pointing to a valid STAR genome index directory.--runThreadN to match available CPU cores; avoid oversubscribing system resources.--genomeSAindexNbases scaled to genome size.