Kallisto and sleuth are recently developed tools for the quantitation and statistical analysis of RNA-Seq data. The tools are fast and accurate, relying on pseudoalignment concepts rather than traditional alignment. They seem to be gaining popularity owing to ease of use and speed that makes them accessible to users on a laptop.
One thing that has been lacking is proper documentation of these tools. This appears to be changing as more tutorials and walkthroughs become available in the past few months.
I wanted to aggregate some of those here for my own reference and also to help others who may be looking for guidance.
kallisto (rapid RNA-Seq read quantification)
kallisto walkthroughs:
kallisto getting started tutorial
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kallisto pachter lab introductory blog post
kallisto videos:
kallisto introduction video tutorial
sleuth (statistical modeling and analysis)
sleuth pachter lab introductory blog post
sleuth walkthroughs:
differential analysis with multiple conditions
sleuth tutorial blog posts:
using kallisto and sleuth (ACHRI bioinformatics)
sample swaps and batch effects (ACHRI bioinformatics)
advanced RNA-Seq modeling of hybrid qualitative/quantitative factors (ACHRI bioinformatics)