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Laptop setup instructions | Griffith Lab

RNA-seq Bioinformatics

Introduction to bioinformatics for RNA sequence analysis

Laptop setup instructions

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 from the Zoom downloads page. If you have Zoom already, please make sure that you update to this particular version as it has functionality we will 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) Download all example scRNAseq files for a loupe demonstration from our course server.

11) 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.

Syntax | Griffith Lab

RNA-seq Bioinformatics

Introduction to bioinformatics for RNA sequence analysis

Syntax

In this tutorial, created using Jekyll (alembic theme) and Kramdown Flavored Markdown, code blocks display commands necessary to complete the tutorial. Some sections are marked as optional and can be skipped.

A code block will look like this:

sudo apt-get install tree
cd ~
# comment
tree -I workspace/student_tools 

All lines contained within the highlighted boxes will need to be executed at the linux command line or an R command prompt (be careful to follow which you should be using). When copy/paste is used, be sure to hit Return or Enter after pasting each command or set of commands. All lines starting with a ‘#’ are comments and will not be interpretted by the shell/R session.