RNA Seq analysis

Welcome to the RAN-Seq analysis wiki!
The organism we will use is liver of cod (gadus morhua).

Reference genome and annotation

Download the reference genome (.fa) and annotation (.gtf) from Ensembl

Genome: wget ftp://ftp.ensembl.org/pub/release-88/fasta/gadus_morhua/dna/Gadus_morhua.gadMor1.dna.toplevel.fa.gz Annotation: wget ftp://ftp.ensembl.org/pub/current_gtf/gadus_morhua/Gadus_morhua.gadMor1.88.gtf.gz

The sequence data

Prepare your .fastq sequence files.

Quality control

FastQC

Download here: http://www.bioinformatics.babraham.ac.uk/projects/download.html#fastqc

Result analysis

http://www.bioinformatics.babraham.ac.uk/projects/fastqc/Help/3%20Analysis%20Modules/
or
https://biof-edu.colorado.edu/videos/dowell-short-read-class/day-4/fastqc-manual

Alignment