STAR (Spliced Transcripts Alignment to a Reference)

Overview

STAR is a splice-aware RNA-seq alignment tool that maps short reads to a reference genome while accurately resolving splice junctions. It uses a suffix array–based approach with two-pass alignment to detect novel splice junctions in the first pass and include them in the genome index for the second pass. STAR is the standard aligner for bulk RNA-seq quantification pipelines (typically paired with RSEM or featureCounts for expression estimation) and supports fusion-gene detection via STARFusion.

Used by

  • Used to align RNA-seq reads to hg38 for 28 metastatic neuroendocrine neoplasms (pog570_bcgsc_2020) in the BC Cancer POG WGTA pipeline; paired with RSEM for transcript-level quantification; expression data drove 6 of 10 clinical benefit outcomes in this cohort PMID:24326773.
  • Used for RNA-seq alignment (STAR v2.3, hg19) in MPNST discovery cohort; enabled detection of SUZ12 structural-variant transcripts missed by WES alone PMID:25240281
  • Used to align RNA-seq reads from 7 uRCC tumours on Illumina HiSeq 2500 to support GSEA-based YAP/TAZ transcriptional signature analysis. PMID:27713405
  • Used STAR aligner for RNA-seq read mapping and splice junction discovery PMID:28373299
  • STAR_2.4.0g1 used for RNA alignment in MET500 transcriptome libraries (868 libraries from 496 tumors) as part of the custom CRISP pipeline with CODAC fusion caller PMID:28783718
  • STAR aligner used to align RNA-seq reads to hg19 in 45 baseline and 26 paired melanoma biopsies from the CA209-038 nivolumab pharmacodynamics study PMID:29033130

Notes

  • STAR requires large memory (typically 30–40 GB RAM for human genome); genome index must be pre-built and is version/annotation-specific.
  • Two-pass mode is recommended to improve sensitivity for novel splice junction detection.
  • Commonly paired with RSEM (transcript-level) or featureCounts/HTSeq (gene-level) for expression quantification.

Sources

This page was processed by entity-page-writer on 2026-05-11. - PMID:25240281

This page was processed by entity-page-writer on 2026-05-11. - PMID:27713405

This page was processed by entity-page-writer on 2026-05-15. - PMID:28373299

This page was processed by wiki-cli on 2026-05-14. - PMID:28783718

This page was processed by entity-page-writer on 2026-05-15. - PMID:29033130

This page was processed by entity-page-writer on 2026-05-15.