ChIP-seq analysis using R - Mapping and file formats

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

Scientific topics: Sequence assembly, RNA-Seq

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

Authors: Anna Poetsch, based partially on material from Ernest Turro University of Cambridge

ChIP-seq analysis using R - Mapping and file formats https://tess.elixir-europe.org/materials/chip-seq-analysis-using-r-mapping-and-file-formats This lecture introduces the principles behind alignment, different tools and de-novo assembly. It also covers post mapping data format and quality control Sequence assembly RNA-Seq ChIP-Seq, RNA-Seq, Alignment, Data-format, Assembly, QC