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Getting started

To get started, if you haven't already, create a new folder for the tutorial and change dir into it:

mkdir genes_tutorial
cd genes_tutorial

Now download the gene annotation file from gencode and place it in that folder. You can either:

  • Download it from the gencode download page for human gene annotations - you want the 'Comprehensive gene annotation' file in GFF3 format.

  • Or download the copy of the gencode file that I have placed in this folder.

For example this command should work to do the download:

curl -O https://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_human/release_41/gencode.v41.annotation.gff3.gz
Note

The file I'll work with below has v41 in the name - as above it's called gencode.v41.annotation.gff3.gz. If you have a different version of this file that's fine - you may get slightly different results below but they should be very similar.