Advancing Epigenetics Towards Systems Biology

Quality Control, trimming and alignment of Bisulfite-Seq data (Prot 57)

Felix Krueger, Simon R Andrews

Introduction

Dramatic improvements and falling costs of high throughput sequencing have made bisulfite sequencing (BS-Seq) a viable option for the global analysis of DNA methylation (Bock et al, 2011; Li et al, 2010; Lister et al, 2009; Lister et al, 2011; Meissner et al, 2008; Stadler et al, 2011; Xie et al, 2012). The analysis of methylation obtained from BS-Seq is relatively straight forward, but care should be taken for initial quality control, trimming and suitable alignment of BS-Seq libraries since these are susceptible to a variety of errors or biases that one could probably get away with in other sequencing applications (discussed in (Krueger et al, 2012)).

This protocol will take you through each of the individual steps we routinely take for BS-Seq or Reduced Representation Bisulfite-Seq (RRBS) data [in our brief guide to RRBS we discuss some additional points that are specifically relevant for RRBS-type experiments (RRBS_Guide)]. Sequencing files that come fresh from the sequencer first undergo (1) initial quality control, are then subjected to (2) quality- and adapter-trimming before (3) the bisulfite reads are aligned to a genome. Optionally, results may be (4) filtered after the alignments have been performed. This procedure yields a final set of methylation data that can be analysed to answer your biological questions of interest.

PDF version

Felix Krueger, Simon R Andrews

Bioinformatics Group, The Babraham Institute, Cambridge, CB22 3AT, United Kingdom

Corresponding author: Felix Krueger & Simon R Andrews
Email feedback to: This email address is being protected from spambots. You need JavaScript enabled to view it.

Felix Krueger and Simon R Andrews
Mon, Jan 21st 2019- Fri, Jan 25th 2019

This meeting will be the first digital health meeting that focuses specifically on the scientific foundations and the health applications of digital technologies. Taking a novel sensor or new device...

Wed, Jan 30th 2019- Thu, Jan 31st 2019

"Conferences Series LLC LTD is organizing “2nd World Congress on Petrochemistry” scheduled to be held during January 30-31,2019, Bangkok, Thailand. The conference invites all the participants across t...

Mon, Feb 25th 2019- Tue, Feb 26th 2019

The seminar will feature approximately 10 talks and 2 poster sessions. All attendees are expected to actively participate in the conference, either by giving an oral presentation or presenting a poste...

Mon, Mar 11th 2019- Tue, Mar 12th 2019

We are pleased to invite you to the upcoming conference 12th World Congress on Cell and Tissue Science scheduled in Singapore on March 11-12,2019. It will bring world-class personalities and researche...

  • Holiday inn Singapore Atrium 317 Outram Road Singapore 169075
  • Organizer

LAST EVENTS

EpiGeneSys Final
Meeting in Paris

Thur. 11 February 2016 - Sat. 13 February 2016

More than 280 scientists attended the fifth Annual Meeting of EpiGeneSys. The conference kicked off with a talk by coordinator Geneviève Almouzni, Director of the Research Center at the Institut Curie, highlighting the achievements of the network over more than five years...

Maison des océans - Paris Read more

PAST EVENTS

The Non-Coding Genome ...

December 3-4 th, 2015

The last training workshop of the EpiGeneSys network

Hotel Mediterraneo - Rome, Italy Read more

Paris / TriRhena Chromatin Club

July 9th, 2015

...exciting talks and network with members of the Chromatin community!

... An EpiGeneSys TAB workshop

June 11st-12nd , 2015

... learn about current approaches to single cell epigenetics and to meet up and network with...

Montpellier, FranceRead more

Latest publications

2017-06-27

The Histone Acetyltransferase Mst2 Protects Active Chromatin from Epigenetic Silencing by Acetylating the Ubiquitin Ligase Brl1.

Read more
2017-05-26

Proliferation Drives Aging-Related Functional Decline in a Subpopulation of the Hematopoietic Stem Cell Compartment.

Read more
2017-04-30

The impact of rare and low-frequency genetic variants in common disease.

Read more