This repository contains code and data for the session on TFBS enrichment. You can download the whole repository using the This bundle of code and data can be downloaded using the button on the top right, either through git at the command line, or as a zip (which then needs to be extracted).
This tutorial uses R and Bioconductor. If you don't have R installed, or you've never used it before, help is available here. I would recommend using Rstudio to run this tutorial. More information about Bioconductor is available on their website.
You need to install some packages first, you can find these in the "install.R" script, which you can run on the command line:
$ Rscript install.R
This requires you to install the Bioconductor package manager if you don't have it already, there is a line you can uncomment to do this. This might take some time, as R packages tend to have a lot of dependencies.
Some data is supplied in data/ and should be found automatically by the notebook.
You will have to download and index the salmon genome (the file is too large to store sensibly in git). You can find in on the Ensembl FTP site here as "Salmo_salar.Ssal_v3.1.dna.toplevel.fa".
Once you have downloaded the genome, you will have to index it using samtools
(the command is samtools faidx Salmo_salar.Ssal_v3.1.dna.toplevel.fa).
You can also simply run the 'get_Ssal_v3.1.R' script to download the genome into 'data/'.