Optimizing RNA-Seq Mapping with STAR

Dobin, A., Gingeras, T. R. (April 2016) Optimizing RNA-Seq Mapping with STAR. Methods Mol Biol, 1415. pp. 245-262. ISSN 1940-6029 (Electronic)1064-3745 (Linking)

URL: http://www.ncbi.nlm.nih.gov/pubmed/27115637
DOI: 10.1007/978-1-4939-3572-7_13


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.

Item Type: Paper
Uncontrolled Keywords: RNA-seq Reads mapping Star Sequence alignment Spliced alignment Transcriptome
Subjects: bioinformatics
bioinformatics > genomics and proteomics
bioinformatics > genomics and proteomics > alignment > sequence alignment
Investigative techniques and equipment > assays > RNA-seq
CSHL Authors:
Communities: CSHL labs > Gingeras lab
CSHL labs > Dobin Lab
CSHL Cancer Center Program > Cancer Genetics and Genomics Program
Depositing User: Matt Covey
Date: April 2016
Date Deposited: 29 Apr 2016 19:34
Last Modified: 05 Nov 2020 21:23
Related URLs:
URI: https://repository.cshl.edu/id/eprint/32644

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