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Prerequisites | Griffith Lab

RNA-seq Bioinformatics

Introduction to bioinformatics for RNA sequence analysis

Prerequisites

Course

Do these before coming to the workshop:

1.) Command line tutorial

You are expected to be familiar with basic command line usage before the workshop. If you are unfamiliar with the command line, below are some suggested tutorials. If you have a Mac computer you can use the “Terminal” application to complete these tutorials. If you have access to a linux server at your institution you could also do them there. If neither of those is available you can try a free online terminal application that runs in your browser such as sandbox.io (also includes several relevant tutorials) or COCALC.

2.) Introduction to R tutorial

Knowing R is critical to this workshop. Using R installed on your computer, please work through the following tutorials (~3 hours).

3.) Reading materials

Please read these articles before coming to the workshop:

Optional readings:

These are just three recently published examples that we find particularly good. We have collected a much more extensive list of resources that should be aware of below. Simply take a look at these and note for future reference.

Course
Laptop setup instructions | Griffith Lab

RNA-seq Bioinformatics

Introduction to bioinformatics for RNA sequence analysis

Laptop setup instructions

Course

Complete the following before coming to the workshop to ensure that your laptop/computer is setup correctly:

1) Install R which can be downloaded from CRAN.

2) Download and install the most recent version of R Studio desktop. If prompted to install git, select yes.

3) Install the BioConductor core packages. Open R or RStudio and at the ‘>’ prompt, paste the commands:

install.packages("BiocManager");
library(BiocManager);
BiocManager::install();

5) Install the Integrative Genomics Viewer 2.8.12 (IGV). Follow the IGV Install Instructions for your operating system.

6) Install an SSH client if needed. Mac users already have a command line ssh program that can be run from the terminal. For Windows users, please download PuTTY.

7) Install Slack. Go to the slack downloads page. Once downloaded, sign into the course slack with the link you received via email.

8) Install or update to Zoom 5.4.2 (or higher) from the Zoom downloads page. If you have Zoom already, please make sure that you update to this particular version (or higher) as it has functionality we may be relying on for this course.

9) Install the Loupe browser. First go to the 10x download pages. Enter your info and select the Loupe Browser 4.0.0 download for your operating system.

10) If relevant to course version, download all example scRNAseq files for a loupe demonstration from our course server.

11) If instructed by email, sign in to the test AWS instance. A security certificate or “key file” and an ip address should have been shared with you via email and slack. Please try to use these to log in to this test AWS instance. Instructions for Mac/Linux users can be found here and instructions for Windows users can be found here.

Course