Mapping RNA‐seq Reads with STAR

Alexander Dobin1, Thomas R. Gingeras1

1 Cold Spring Harbor Laboratory, Cold Spring Harbor, New York
Publication Name:  Current Protocols in Bioinformatics
Unit Number:  Unit 11.14
DOI:  10.1002/0471250953.bi1114s51
Online Posting Date:  September, 2015
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Abstract

Mapping of large sets of high‐throughput sequencing reads to a reference genome is one of the foundational steps in RNA‐seq data analysis. The STAR software package performs this task with high levels of accuracy and speed. In addition to detecting annotated and novel splice junctions, STAR is capable of discovering more complex RNA sequence arrangements, such as chimeric and circular RNA. STAR can align spliced sequences of any length with moderate error rates, providing scalability for emerging sequencing technologies. STAR generates output files that can be used for many downstream analyses such as transcript/gene expression quantification, differential gene expression, novel isoform reconstruction, and signal visualization. In this unit, we describe computational protocols that produce various output files, use different RNA‐seq datatypes, and utilize different mapping strategies. STAR is open source software that can be run on Unix, Linux, or Mac OS X systems. © 2015 by John Wiley & Sons, Inc.

Keywords: sequence alignment; reads mapping; RNA‐seq; transcriptome; spliced alignment; STAR

     
 
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Table of Contents

  • Introduction
  • Basic Protocol 1: Mapping RNA‐seq Reads to the Reference Genome
  • Alternate Protocol 1: Generating Genome Indices
  • Alternate Protocol 2: Mapping RNA‐seq Reads with 2‐Pass Procedure
  • Alternate Protocol 3: Mapping Reads and Generating Unsorted and Coordinate‐Sorted BAM Files
  • Alternate Protocol 4: Generating Signal Files for Visualization on Genome Browsers for Stranded RNA‐seq Data
  • Alternate Protocol 5: Generating Signal Files for Visualization on Genome Browsers for Un‐Stranded RNA‐seq Data
  • Alternate Protocol 6: Mapping RNA‐seq Reads and Generating Chimeric Alignments to Detect Fusion Transcripts and Circular RNA
  • Alternate Protocol 7: Mapping RNA‐seq Reads, Generating Output in Transcriptomic Coordinates and using RSEM to Quantify Expression of Transcripts and Genes
  • Alternate Protocol 8: Mapping RNA‐seq Reads and Running Cufflinks to Assemble and Quantify Transcripts for Stranded RNA‐seq Data
  • Alternate Protocol 9: Mapping RNA‐seq Reads and Running Cufflinks to Assemble and Quantify Transcripts for Un‐Stranded RNA‐seq Data
  • Support Protocol 1: Downloading and Installing Star
  • Support Protocol 2: Downloading PRE‐Built Genome Indices
  • Guidelines for Understanding Results
  • Commentary
  • Figures
  • Tables
     
 
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Materials

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Figures

Videos

Literature Cited

Literature Cited
  Dobin, A., Davis, C.A., Schlesinger, F., Drenkow, J., Zaleski, C., Jha, S., Batut, P., Chaisson, M., and Gingeras, T.R. 2013. STAR: Ultrafast universal RNA‐seq aligner. Bioinformatics 29:15‐21. doi: 10.1093/bioinformatics/bts635.
  Li, B. and Dewey, C.N. 2011. RSEM: Accurate transcript quantification from RNA‐Seq data with or without a reference genome. BMC Bioinformatics 12:323.
  Li, H., Handsaker, B., Wysoker, A., Fennell, T., Ruan, J., Homer, N., Marth, G., Abecasis, G., and Durbin, R. 2009. The sequence alignment/map format and SAMtools. Bioinformatics 25:2078‐2079. doi: 10.1093/bioinformatics/btp352.
  Trapnell, C., Williams, B.A., Pertea, G., Mortazavi, A., Kwan, G., van Baren, M.J., Salzberg, S.L., Wold, B.J., and Pachter, L. 2010 Transcript assembly and quantification by RNA‐Seq reveals unannotated transcripts and isoform switching during cell differentiation. Nat. Biotechnol. 28:511‐515. doi: 10.1038/nbt.1621.
Internet Resources
  https://github.com/alexdobin/STAR
  GitHub STAR code repository: the best place to obtain the latest versions of the source code, executables, and documentation.
  https://groups.google.com/forum/#!forum/rna‐star
  STAR user discussion group: the best place to ask questions and obtain help from the authors and other users.
  https://github.com/alexdobin/STAR/raw/master/doc/STARmanual.pdf
  STAR manual containing detailed information on all options, output, and formatting. This file is also a part of the STAR source code distribution.
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