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: [email protected], [email protected]
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 (www.rnaseq.wiki)
This includes all [[figures|https://github.com/griffithlab/rnaseq_tutorial/tree/master/manuscript/figures]] and [[supplementary tables|https://github.com/griffithlab/rnaseq_tutorial/tree/master/manuscript/supplementary_tables]].
- [[Figure 1|https://github.com/griffithlab/rnaseq_tutorial/blob/master/manuscript/figures/Figure1.pdf]] - An overview of the central dogma of molecular biology
- [[Figure 2|https://github.com/griffithlab/rnaseq_tutorial/blob/master/manuscript/figures/Figure2.pdf]] - RNA-seq data generation
- [[Figure 3|https://github.com/griffithlab/rnaseq_tutorial/blob/master/manuscript/figures/Figure3.pdf]] - RNA-seq library fragmentation and size selection strategies that influence interpretation and analysis
- [[Figure 4|https://github.com/griffithlab/rnaseq_tutorial/blob/master/manuscript/figures/Figure4.pdf]] - RNA-seq library enrichment strategies that influence interpretation and analysis
- [[Figure 5|https://github.com/griffithlab/rnaseq_tutorial/blob/master/manuscript/figures/Figure5.pdf]] - RNA-seq analysis flow-chart
- [[Figure 6|https://github.com/griffithlab/rnaseq_tutorial/blob/master/manuscript/figures/Figure6.pdf]] - Comparison of stranded and unstranded RNA-seq library methods and their influence on interpretation and analysis
- [[Supplementary Table 1 |https://github.com/griffithlab/rnaseq_tutorial/blob/master/manuscript/supplementary_tables/supplementary_table_1_urls.md]] - RNA-seq analysis techniques
- [[Supplementary Table 2 |https://github.com/griffithlab/rnaseq_tutorial/blob/master/manuscript/supplementary_tables/supplementary_table_2_urls.md]] - Tools for RNA-seq analysis
- [[Supplementary Table 3 |https://github.com/griffithlab/rnaseq_tutorial/blob/master/manuscript/supplementary_tables/supplementary_table_3.md]] - Concepts in sample preparation and library construction that can influence study design, analysis and interpretation
- [[Supplementary Table 4 |https://github.com/griffithlab/rnaseq_tutorial/blob/master/manuscript/supplementary_tables/supplementary_table_4.md]] - Description of RNA-seq library enrichment strategies
- [[Supplementary Table 5 |https://github.com/griffithlab/rnaseq_tutorial/blob/master/manuscript/supplementary_tables/supplementary_table_5.md]] - Strand related settings for RNA-seq tools that must be adjusted to account for library construction strategy
- [[Supplementary Table 6 |https://github.com/griffithlab/rnaseq_tutorial/blob/master/manuscript/supplementary_tables/supplementary_table_6.md]] - Standard file formats and tool-specific files used in RNA-seq analysis
- [[Supplementary Table 7 |https://github.com/griffithlab/rnaseq_tutorial/blob/master/manuscript/supplementary_tables/supplementary_table_7.md]] - Common RNA-seq questions and their answers
- [[Supplementary Table 8 |https://github.com/griffithlab/rnaseq_tutorial/blob/master/manuscript/supplementary_tables/supplementary_table_8.md]] - Resources for RNA-seq analysis
- [[Supplementary Table 9 |https://github.com/griffithlab/rnaseq_tutorial/blob/master/manuscript/supplementary_tables/supplementary_table_9.md]] - RNA-seq workshops and online tutorials
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