Use when aligning long RNA-seq reads (PacBio, Nanopore) to a reference genome using splice-aware mapping with STARlong.
STARlong-plain --genomeDir /path/to/index --readFilesIn reads.fastq/home/vimalinx/miniforge3/envs/bio/bin/STARlong-plainreferences/help.md for complete options and parameters# 1) Build a genome index for STARlong
STARlong-plain \
--runMode genomeGenerate \
--genomeDir starlong_index \
--genomeFastaFiles genome.fa \
--sjdbGTFfile genes.gtf \
--runThreadN 16
# 2) Align long reads from FASTQ
STARlong-plain \
--genomeDir starlong_index \
--readFilesIn longreads.fastq \
--runThreadN 16
# 3) Align gzipped long reads and emit sorted BAM
STARlong-plain \
--genomeDir starlong_index \
--readFilesIn longreads.fastq.gz \
--readFilesCommand zcat \
--outSAMtype BAM SortedByCoordinate \
--runThreadN 16
STARlong-plain --runMode genomeGenerate --genomeDir ./index --genomeFastaFiles genome.fa --sjdbGTFfile annotations.gtfSTARlong-plain --genomeDir ./index --readFilesIn reads.fastq--genomeSAindexNbases may need scaling for small genomes: min(14, log2(GenomeLength)/2 - 1)--sysShell /bin/bash if default shell fails--readFilesCommand zcat or an equivalent decompressor