ChIP-seq analysis using R - Mapping and file formats

Keywords

ChIP-Seq, RNA-Seq, Alignment, Data-format, Assembly, QC

Authors

• Anna Poetsch
• based partially on material from Ernest Turro (University of Cambridge)

Type

• Lecture

Description

This lecture introduces the principles behind alignment, different tools and de-novo assembly. It also covers post mapping data format and quality control

Aims

The aim of the course is to introduce the principles for aligning reads to a genome or transcriptome and gives a selection of tools that are commonly used for these tasks. It introduces the data formats involved and covers post alignment quality control.

Prerequisites

• HTS-introduction

Target audience

Biologist, Computational biologist

Learning objectives

• Understand the principles of aligning reads to genomes or transcriptomes
• Get familiar with some commonly used tools
• understand the data formats after alignment
• understand post alignment quality control and associated tools

Materials

• not applicable

Data

• not applicable

Timing

1 hour

Content stability

Stable. There might be small updates in the future.

Technical requirements

• None

Literature references