ChIP-seq analysis using R - File formats and QC

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

Scientific topics: RNA-Seq

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

Authors: Anna Poetsch

ChIP-seq analysis using R - File formats and QC https://tess.elixir-europe.org/materials/chip-seq-analysis-using-r-file-formats-and-qc 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. RNA-Seq ChIP-Seq, RNA-Seq, QC, Data-format, Experimental-design