STAR Aligner

Overview

STAR (Spliced Transcripts Alignment to a Reference) is a high-speed RNA-seq read aligner that handles spliced alignments across intron-exon boundaries and chimeric reads spanning gene fusions. It uses a seed-search-extension strategy to align reads efficiently to large genomes. STAR is widely used as the primary alignment step for RNA-seq pipelines that include fusion detection (STAR-Fusion) or quantification (RSEM).

Used by

• Used for RNA-seq alignment in AALE chr_3p-deleted cell experiments (HiSeq 2500 PE100) as part of the STAR + RSEM + edgeR pipeline for differential expression analysis PMID:29622463

Notes

• STAR generates chimeric alignment output that STAR-Fusion uses for fusion detection.
• Requires 2-pass mapping mode for optimal splice-junction detection in RNA-seq.
• High memory requirements (~30 GB for human genome index).

Sources

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