Use when aligning long RNA-seq reads to a reference genome or generating genome indexes for spliced transcript alignment
STARlong-sse4.1/home/vimalinx/miniforge3/envs/bio/bin/STARlong-sse4.1references/help.md for complete parameter documentation# 1) Build a genome index for STARlong
STARlong-sse4.1 \
--runMode genomeGenerate \
--genomeDir starlong_index \
--genomeFastaFiles genome.fa \
--sjdbGTFfile genes.gtf \
--runThreadN 16
# 2) Align long reads from FASTQ
STARlong-sse4.1 \
--genomeDir starlong_index \
--readFilesIn longreads.fastq \
--runThreadN 16
# 3) Align gzipped long reads and emit sorted BAM
STARlong-sse4.1 \
--genomeDir starlong_index \
--readFilesIn longreads.fastq.gz \
--readFilesCommand zcat \
--outSAMtype BAM SortedByCoordinate \
--runThreadN 16
STARlong-sse4.1 --runMode genomeGenerate --genomeDir /path/to/index --genomeFastaFiles ref.fa --sjdbGTFfile annotations.gtfSTARlong-sse4.1 --genomeDir /path/to/index --readFilesIn reads.fq --runThreadN N--genomeSAindexNbases down for small genomes (min(14, log2(GenomeLength)/2 - 1))--readFilesType (default Fastx for FASTA/FASTQ)