ChIP-seq analysis using R - File formats and QC

Keywords

ChIP-Seq, RNA-Seq, QC, Data-format, Experimental-design

Authors

• Anna Poetsch

Type

• Lecture

Description

This lecture introduces the file formats of sequencing data before alignment and covers the general quality control of sequencing data focussing on RNA-Seq and ChIP-Seq.

Aims

The aim of the course is to introduce, what information is contained in sequencing data fefore alignmant and goes step by step through a standard quality control pipeline. It gives examples, how good and bad data look like and what kind of problems one can encounter.

Prerequisites

• HTS-introduction

Target audience

Biologist, Computational biologist

Learning objectives

• Understand file formats before the alignment
• Understand how to perform quality control on read data
• Get a feeling of what "good" and "bad" data look like

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