Optimizing RNA-Seq Mapping with STAR.
Recent advances in high-throughput sequencing technology made it possible to probe the cell transcriptomes by generating hundreds of millions of short reads which represent the fragments of the transcribed RNA molecules. The first and the most crucial task in the RNA-seq data analysis is mapping of the reads to the reference genome. STAR (Spliced Transcripts Alignment to a Reference) is an RNA-seq mapper that performs highly accurate spliced sequence alignment at an ultrafast speed. STAR alignment algorithm can be controlled by many user-defined parameters. Here, we describe the most important STAR options and parameters, as well as best practices for achieving the maximum mapping accuracy and speed.
Cold Spring Harbor Laboratory, One Bungtown Road, Cold Spring Harbor, NY, 11746, USA. dobin@cshl.edu.
Alexander
A
Dobin
Cold Spring Harbor Laboratory, One Bungtown Road, Cold Spring Harbor, NY, 11746, USA.
Thomas R
TR
Gingeras
D000465:Algorithms; D019295:Computational Biology / Q000379:methods; D020869:Gene Expression Profiling / Q000379:methods*; D006801:Humans; D012326:RNA Splicing; D016415:Sequence Alignment / Q000379:methods; D017423:Sequence Analysis, RNA / Q000379:methods*; D014584:User-Computer Interface
RNA-seq; Reads mapping; STAR; Sequence alignment; Spliced alignment; Transcriptome