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

Goal¶

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

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

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)

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

Note

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

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.

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