RNA Sequencing - Your own pipeline from scratch
3 videos • 2,685 views • by Danny Arends Learn how to build a computational RNA sequencing pipeline from scratch using free and open source bioinformatics software. The first stream will teach you how to setup your Linux environment (using VirtualBox) and is a step by step guide on how to install all tools required for RNA-Seq analysis: Trimmomatic, STAR, HTSlib, BCFtools, samtools, GATK, and the SRAtoolkit. The second stream uses R to download the Saccharomyces cerevisiae genome, transcriptome, and known SNPs from the Ensembl database. We use a publicly available paired-end RNA-Seq data set from the Sequence Read Archive (SRA) to develop and test our FASTQ to BAM pipeline in R. Learn about Alignment, Read trimming, and Quality Checks of RNA Sequencing data. Third stream will show how to extract read counts and compute RPKM/FPKM values using R. We use statistics to compute differential gene expression and use several visualizations, such as a volcano plot and heatmaps to visualize this. We annotated differentially expressed genes using biomaRt and perform pathway over-representation analysis using DAVID (Database for Annotation, Visualization and Integrated Discovery) 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 #RNAseq #RNASequencing #transcriptomics #geneexpression #differentialgeneexpression #pathwayanalysis #bioinformatics #computationalbiology #dataanalysis #visualization