RNA Sequencing - Setup and Prerequisites
Channel: Danny Arends
Date: 2022-10-09

Learn how to create a computational RNA sequencing pipeline using free and open source bioinformatics software. During this live stream I'll teach you how to use VirtualBox to setup a Linux environment within windows. This first stream will be a step by step explanation on how to install all the tools required for RNA-Seq analysis (Trimmomatic, STAR, HTSlib, BCFtools, samtools, GATK, SRAtoolkit). 

If we have enough time, we will download a _Saccharomyces cerevisiae_ genome and transcriptome from Ensembl and use a publicly available data set from the Sequence Read Archive (SRA) to develop and test our pipeline in R, a free software environment for statistical computing and graphics.

Code on GitHub: https://gist.github.com/DannyArends/04d87f5590090dfe0dc6b42e5e1bbe15
Presentation on OneDrive: https://1drv.ms/b/s!AtYWSYRMmSHZh4gFsR1904Y-Cce04Q?e=Q8dtRl

Thanks for taking an interest in my channel 😄If you've made it this far down, support me by giving a like or subscribing. Join me during my live streams Thursday afternoons on YouTube or follow me on Twitch @ https://www.twitch.tv/dannyarends

Chapters:
00:00:00 - Sound check and introduction
00:01:52 - Overview
00:04:18 - Setup VirtualBox and create a Virtual HDD
00:13:50 - Setup the Virtual Machine for Debian
00:16:30 - Installing Debian into the Virtual Machine
00:35:25 - VirtualBox extensions and Guest Additions
00:44:00 - Tools for the RNA Sequencing pipeline
00:47:47 - Download and install R and R packages
00:56:02 - Installing Trimmomatic from source
01:02:20 - Installing the STAR RNA-seq aligner
01:13:32 - Installing PICARD from source
01:17:19 - Installing HTSlib, samtools, and bcftools
01:27:39 - Installing GATK (v4.2)
01:33:36 - The SRAtoolkit install and config
01:50:19 - Creating a bin/ folder and updating our PATH
02:00:02 - The reference genome & Transcriptome
02:07:15 - Overview for the next stream

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