Tutorial on (s)BLISS Downstream Analysis

Welcome to this tutorial. The aim is to provide a guide to the preliminary downstream analysis of (s)BLISS data. A Nature Protocols article provides a summary of the sBLISS technology and a walkthrough on the analysis of the results.

Getting Started

Requirements

In order to run this tutorial, the following tools are needed:

• Internet connection (to dynamically retrieve the ENSEMBL reference annotation)
• R >= 3.6.0
• Installed R packages: GenomicFeatures, AnnotationHub, biomaRt, rtracklayer, data.table, circlize, ComplexHeatmap, ggplot2, ggpubr, ggsci

Setup

First, clone this repository on your computer and move to the new directory:

git clone git@github.com:BiCroLab/blissNPanalysis.git

cd blissNPanalysis

This tutorial assumes that the BED files required for its correct execution, which can be downloaded from here, are located in the ./data folder.

Once the data has been downloaded or moved to the data folder, open R and continue to either of the following sections:

• Human TK6 sBLISS analysis
• Mouse enterocyte sBLISS analysis