rnaseq-kallisto

This pipeline performs the following task processes RNA seq data using kallisto for mapping

• perform quality control on FastQ files using FastQC
• view quality of reads using MultiQC
• align reads of each sample in a run against reference genome (using kallisto)
• count reads in features (using HTSeq-count)
• normalize read counts (using DESeq)
• calculate RPKMs (using edgeR)
• perform DE analysis for standard designs (using DESeq2)

Downloading and installing

Clone this repository:

git clone --recurse-submodules https://github.com/tobbyxy/rnaseq-kallisto
cd rnaseq-kallisto

Create and activate a Conda environment with all the required software dependencies:

conda env setup -f environment.yml
conda activate rnaseq-kallisto

Setting up a genomic reference

This tutorial uses a human reference from Ensembl, you can download by heading to

• https://ftp.ensembl.org/pub/release-108/fasta/homo_sapiens/cdna/Homo_sapiens.GRCh38.cdna.all.fa.gz

To build index run the kallisto script or run

kallisto index -i Homo_sapiens.GRCh38.cdna.all.index Homo_sapiens.GRCh38.cdna.all.fa 

To do

Update scripts to include

• normalize read counts (using DESeq)
• calculate RPKMs (using edgeR)
• perform DE analysis (using DESeq2)