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#0-ii. Citation and description of published materials
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*. Informatics for RNA-seq: A web resource for analysis on the cloud. In preparation.
*To whom correspondence should be addressed: E-mail: mgriffit[AT]genome.wustl.edu, ogriffit[AT]genome.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,
Figure 2,
Figure 3,
Figure 4,
Figure 5,
Figure 6
Supplementary Table 1,
Supplementary Table 2,
Supplementary Table 3
Supplementary Table 4,
Supplementary Table 5,
Supplementary Table 6
| Previous Section | This Section | Next Section | |:-----------------------------:|:---------------------------:|:-----------------------:| | Authors | Citation | Syntax |
NOTICE: This resource has been moved to rnabio.org. The version here will be maintained for legacy use only. All future development and maintenance will occur only at rnabio.org. Please proceed to rnabio.org for the current version of this course.
Table of Contents
Module 0: Authors | Citation | Syntax | Intro to AWS | Log into AWS | Unix | Environment | Resources
Module 1: Installation | Reference Genomes | Annotations | Indexing | Data | Data QC
Module 2: Adapter Trim | Alignment | IGV | Alignment Visualization | Alignment QC
Module 3: Expression | Differential Expression | DE Visualization
Module 4: Alignment Free - Kallisto
Module 5: Ref Guided | De novo | Merging | Differential Splicing | Splicing Visualization
Module 6: Trinity
Module 7: Trinotate
Appendix: Saving Results | Abbreviations | Lectures | Practical Exercise Solutions | Integrated Assignment | Proposed Improvements | AWS Setup