Useful links for Kallisto and Sleuth RNA-seq analysis

I recently compiled a list of websites that are very useful for me to understand the Kallisto and Sleuth RNA-seq workflow.

First, we should always check the official resources first.

  • https://pachterlab.github.io/sleuth/walkthroughs

Some walk-through examples.

  • https://groups.google.com/forum/#!forum/kallisto-sleuth-users

User group support for Sleuth

  • https://github.com/pachterlab/sleuth/issues

Reported issues with Sleuth

  • https://galaxyproject.org/tutorials/rb_rnaseq/

Below are some resources I collected while I learn about RNA-seq analysis and Kallisto/Sleuth analysis

Tutorial for RNA-seq, introducing basic principles of experiment and theory and common computational software for RNA-seq.

  • http://chagall.med.cornell.edu/RNASEQcourse/

This page contains very detailed introductory documents about RNA-seq analysis.

  • https://scilifelab.github.io/courses/rnaseq/labs/kallisto

Tutorials for running Kallisto and Sleuth. These tutorials focus on the overall workflow, with little emphasis on complex, multi-factorial experimental design of RNA-seq.

  • https://hbctraining.github.io/In-depth-NGS-Data-Analysis-Course/sessionIV/lessons/02_sleuth.html

Excellent tutorial for Sleuth analysis after Kallisto quantification of transcripts.

  • https://informatics.fas.harvard.edu/workshops/HarvardInformatics_DEworkshop_Fall2017.html

Another excellent tutorial for Sleuth analysis.

  • http://achri.blogspot.com/2017/03/this-is-not-normal-dealing-with.html
  • http://achri.blogspot.com/2016/10/using-kallisto-sleuth.html
  • http://achri.blogspot.com/2017/02/modelling-rnaseq-like-car-in-traffic.html
  • http://achri.blogspot.ca/2016/02/how-not-to-use-deseq2-for-illumina.html

A few very informative blogs about using Sleuth in for more challenging RNA-seq situation

  • http://faculty.chicagobooth.edu/richard.hahn/teaching/formulanotation.pdf

Lastly, a document for how interaction is specified in R, which is applicable to Sleuth for specifying experimental design formula.

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