Introduction

In this post, I will show how easy it is to extract the genomic positions of every promoters of a specific genome build.

For this demo, you will need the TxDb.Hsapiens.UCSC.hg19.knownGene package:

The goal of this post is to show how to import narrowPeak and broadPeak files into R in a valid GRanges format.

To do so, you need to have installed the rtracklayer package. To replicate the examples in this document, you will also need to install the GenomicFormatExamples package.

Introduction

In this document, we will see how to slice a genome. More specifically, we will extract all the aligned regions with a coverage greater than 0. This can be useful if we want to focus with genomic regions where some reads were aligned and to discard all the empty regions.

Dataset presentation

We will work with the packages pasillaBamSubset that has reads only on chr4.