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RNA-Seq Basics: Generating and processing raw sequence data using Nanopore and CyVerse


In this quick start, we will show you how to launch JupyterLab-QIIME2 VICE app in DE


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 Register


We will use the following CyVerse platform(s):

Platform Interface Link Platform Documentation Learning Center Docs
Discovery Environment Web/Point-and-click Discovery Environment DE Manual Guide

Input and example data

In order to complete this quickstart you will need to have the following inputs prepared

Input File(s) Format Preparation/Notes Example Data
Sequencing reads FastQ Any sequencing reads in FastQ format will work. They do not need to be pre-processed. They may also be compressed (e.g. fastq.gz) gut microbiome (iplantcollaborative > example_data > qiime2 and select gut-microbiome folder)

Get started: Launch JupyterLab-QIIME2

  1. Click this button to launch RStudio-DESeq2 app in DE
  1. Under “Analysis Name” leave the defaults or make any desired notes.
  2. Click Launch Analysis. You will receive a notification that the job has been submitted and running with the “Access your running analysis here”.
  3. Clicking on the “Access your running analysis” will open the RStudio in another tab in the browser after a brief building phase.


You will be asked to authenticate to the Rstudio using username rstudio and password rstudio

  1. Finally, once you finish analysis, navigate to the DE tab, select the Analysis window and select the analysis, click “save and complete analysis”. Upon clicking complete analysis, the analysis will be completed and all the outputs will be brought back to the analysis folder.

Additional information, help

  • Full materials for the webinar is available here
  • See the original JupyterLab quick start
  • See the original qiime2.org for how to run qiime2 analysis
  • Contact CyVerse support by clicking the intercom button on the page.

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