Syntax

In this tutorial, created using Jekyll (alembic theme) and Kramdown Flavored Markdown, code blocks display commands necessary to complete the tutorial. Some sections are marked as optional and can be skipped.

A code block will look like this:

sudo apt-get install tree
cd ~
# comment
tree -I workspace/student_tools

All lines contained within the highlighted boxes will need to be executed at the linux command line or an R command prompt (be careful to follow which you should be using). When copy/paste is used, be sure to hit Return or Enter after pasting each command or set of commands. All lines starting with a ‘#’ are comments and will not be interpretted by the shell/R session.

Citation

« Introduction to RNA-seq and course setup Course Syntax »

This tutorial is accompanied by a publication. If you find the materials here or in that paper useful, please cite the following: Malachi Griffith*, Jason R. Walker, Nicholas C. Spies, Benjamin J. Ainscough, Obi L. Griffith*. 2015. Informatics for RNA-seq: A web resource for analysis on the cloud. PLoS Comp Biol. 11(8):e1004393. *To whom correspondence should be addressed: E-mail: mgriffit@wustl.edu, obigriffith@wustl.edu

All materials associated with this publication, including high resolution and original figure files, supplementary tables, etc. are available here: https://github.com/griffithlab/rnaseq_tutorial

This includes all figures and supplementary tables.

Figure 1 - An overview of the central dogma of molecular biology
Figure 2 - RNA-seq data generation
Figure 3 - RNA-seq library fragmentation and size selection strategies that influence interpretation and analysis
Figure 4 - RNA-seq library enrichment strategies that influence interpretation and analysis
Figure 5 - RNA-seq analysis flow-chart
Figure 6 - Comparison of stranded and unstranded RNA-seq library methods and their influence on interpretation and analysis
Supplementary Table 1 - RNA-seq analysis techniques
Supplementary Table 2 - Tools for RNA-seq analysis
Supplementary Table 3 - Concepts in sample preparation and library construction that can influence study design, analysis and interpretation
Supplementary Table 4 - Description of RNA-seq library enrichment strategies
Supplementary Table 5 - Strand related settings for RNA-seq tools that must be adjusted to account for library construction strategy (See Strand Settings page for most current version of this information)
Supplementary Table 6 - Standard file formats and tool-specific files used in RNA-seq analysis
Supplementary Table 7 - Common RNA-seq questions and their answers
Supplementary Table 8 - Resources for RNA-seq analysis
Supplementary Table 9 - RNA-seq workshops and online tutorials

« Introduction to RNA-seq and course setup Course Syntax »

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