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BioInfoSummer18 - Advanced Kallisto RNA-Seq (Bulk and Single Cell)

Goal

This draft tutorial will introduce some of the features of the Kallisto and Sleuth tools for RNA-Sequencing of bulk and single-cell samples.

Warning

This tutorial is still in its draft form. These datasets are not yet available on the CyVerse Data Store, but are available on an Amazon AMI and docker container. These will later be migrated to VICE. Additionally, these materials are part of a workshop collection and not yet designed for independent use. These should not be relied on for analysis of your own data - they are merely useful examples that can inform your own analysis.


Prerequisites

Downloads, access, and services

In order to complete this tutorial you will need access to the following services/software

Prerequisite Preparation/Notes Link/Download
CyVerse account You will need a CyVerse account to complete this exercise CyVerse User Portal
Docker You must have access to Docker to run this tutorial Dockerhub
Amazon AWS Account You can run this tutorial from this AMI: ami-042909f3c5b9bf6ed

Platform(s)

We will use the following CyVerse platform(s):

Platform Interface Link Platform Documentation Quick Start
Data Store GUI/Command line Data Store Data Store Manual Data Store Guide
Discovery Environment Web/Point-and-click Discovery Environment DE Manual Discovery Environment Guide
VICE A flexible environment for using Jupyterlab, RStudio, and RShiny   Vice Documentation