/RNA-seq_data_analysis_course_for_biologists_may_2018

The goal of the course is to introduce basic RNA-seq data analysis, starting from experiment design and raw files to functional data analysis that can be performed using PC only. In brief, the content of the course will cover: general knowledge on RNA-seq library preparation (which kit/technology should I use and why? how many replicates? how deep should I sequence my samples?), quality check and filtering of the reads (including adapter trimming, rRNA removal), read alignment/quasi-mapping (can I perform read mapping on my PC without losing its specificity and efficacy?), performing gene counts (assigning reads to provided gene annotation), data normalization (which normalization types should I apply to my data?), differential expression data analysis, basic data visualization, functional analysis (GO terms, pathway analysis).

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RNA-seq data analysis course for biologists - README

This repository is short RNA-seq workshop covering one of the simplest workflows starting with data download and finishing at differential expression calling.

Overview

The tutorial.rst file covers the first part of our workshops, while workshop.sh is basicaly solution of this part (TODO).

Downloading the raw data

This repository contains just tutorial materials and solution script that can perform all covered analysis. To download raw data use script download_raw_data.sh that can be find in main directory.

Dependecies

Tutorial assumes that user have access to following programs and packages: + fastq-dump + fastqc + multiqc + cutadapt + salmon + R