Upcoming Workshop: A Practical Introduction to NGS Data Analysis (Oxford, UK)

ecSeq Bioinformatics · 10-27-2014, 06:14 AM

A Practical Introduction to NGS Data Analysis

13-14 April 2015

Link to Workshop Page

Number of Available Spaces: 28

Venue: ISIS Room, Oxford University IT Services, 7-19 Banbury Road, Oxford OX2 6NN, UK

The purpose of this workshop is to get a deeper understanding in High-Throughput Sequencing (HTS) with a special focus on bioinformatics issues. Advantages and disadvantages of current sequencing technologies and their implications on data analysis will be discovered. The participants will be trained on understanding their own HTS data, finding potential problems/errors therein and finally performing their own analyses using open source tools. In the course we will use a RNA-seq dataset from the current market leader, Illumina.

Each participant will have a dedicated workstation for the training.

Workshop Programme:

Day 1: 13 April, Monday: 9.00-17.00 (including two refreshment breaks and a lunch break)

Introduction to sequencing technologies from a data analysts viewSequence file formats (fastq)
Mechanisms of instruments: Illumina, 454, IonTorrent and PacBio
Sequencing protocols (mRNA-seq, microRNAseq, …)
Capabilities & limitations: Error sources, biases & beyond
Preparation of raw reads: quality control, adapter clipping
Read mapping
Alignment methods
Mapping tools, mapping to a reference genome

Day 2: 14 April, Tuesday: 9.00-17.00 (including two refreshment breaks and a lunch break)

Mapping output
File formats (SAM/BAM)
Samtools
Bedtools
Visualization of mapped reads
UCSC: Data format for upload
IGV
Gene expression quantification
Differential expression analysis

ecSeq Bioinformatics • Brandvorwerkstr. 43, D-04275 Leipzig, Germany • www.ecSeq.com

ecSeq Bioinformatics · 04-01-2015, 05:10 AM

Last Day to Register!

Go to: http://lpmhealthcare.com/ngs-workshop-2015-oxford/

ecSeq Bioinformatics · 06-21-2015, 10:41 PM

UPDATE:

There will be a epigenetics workshop in December (visit http://www.ecseq.com/workshops/workshop_2015-02.html)
There will be another RNA-Seq workshop in January or February 2016 (to get a notification once the date is fix, you can sign up for our newsletter at www.ecseq.com)
We also offer 'On-Site Bioinformatics Courses', which might be of interest to you and/or your institute (visit http://www.ecseq.com/workshops/on-site-courses.html to get more information)

ecSeq Bioinformatics · 06-29-2015, 03:08 AM

Upcoming workshop: A Beginner's Guide to RNA-Seq Data Analysis

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10-27-2014, 06:14 AM	#1
ecSeq Bioinformatics Senior Member Location: Leipzig, Germany Join Date: May 2012 Posts: 271	Upcoming Workshop: A Practical Introduction to NGS Data Analysis (Oxford, UK) A Practical Introduction to NGS Data Analysis 13-14 April 2015 Link to Workshop Page Number of Available Spaces: 28 Venue: ISIS Room, Oxford University IT Services, 7-19 Banbury Road, Oxford OX2 6NN, UK The purpose of this workshop is to get a deeper understanding in High-Throughput Sequencing (HTS) with a special focus on bioinformatics issues. Advantages and disadvantages of current sequencing technologies and their implications on data analysis will be discovered. The participants will be trained on understanding their own HTS data, finding potential problems/errors therein and finally performing their own analyses using open source tools. In the course we will use a RNA-seq dataset from the current market leader, Illumina. Each participant will have a dedicated workstation for the training. Workshop Programme: Day 1: 13 April, Monday: 9.00-17.00 (including two refreshment breaks and a lunch break) Introduction to sequencing technologies from a data analysts viewSequence file formats (fastq) Mechanisms of instruments: Illumina, 454, IonTorrent and PacBio Sequencing protocols (mRNA-seq, microRNAseq, …) Capabilities & limitations: Error sources, biases & beyond Preparation of raw reads: quality control, adapter clipping Read mapping Alignment methods Mapping tools, mapping to a reference genome Day 2: 14 April, Tuesday: 9.00-17.00 (including two refreshment breaks and a lunch break) Mapping output File formats (SAM/BAM) Samtools Bedtools Visualization of mapped reads UCSC: Data format for upload IGV Gene expression quantification Differential expression analysis ecSeq Bioinformatics • Brandvorwerkstr. 43, D-04275 Leipzig, Germany • www.ecSeq.com __________________ ecSeq Bioinformatics is Europe’s leading provider of hands-on bioinformatics workshops and professional data analysis in the field of Next-Generation Sequencing (NGS). Last edited by ecSeq Bioinformatics; 02-11-2015 at 12:05 AM.

04-01-2015, 05:10 AM	#2
ecSeq Bioinformatics Senior Member Location: Leipzig, Germany Join Date: May 2012 Posts: 271	Last Day to Register! Go to: http://lpmhealthcare.com/ngs-workshop-2015-oxford/ __________________ ecSeq Bioinformatics is Europe’s leading provider of hands-on bioinformatics workshops and professional data analysis in the field of Next-Generation Sequencing (NGS).

06-21-2015, 10:41 PM	#3
ecSeq Bioinformatics Senior Member Location: Leipzig, Germany Join Date: May 2012 Posts: 271	UPDATE: There will be a epigenetics workshop in December (visit http://www.ecseq.com/workshops/workshop_2015-02.html) There will be another RNA-Seq workshop in January or February 2016 (to get a notification once the date is fix, you can sign up for our newsletter at www.ecseq.com) We also offer 'On-Site Bioinformatics Courses', which might be of interest to you and/or your institute (visit http://www.ecseq.com/workshops/on-site-courses.html to get more information) __________________ ecSeq Bioinformatics is Europe’s leading provider of hands-on bioinformatics workshops and professional data analysis in the field of Next-Generation Sequencing (NGS).

06-29-2015, 03:08 AM	#4
ecSeq Bioinformatics Senior Member Location: Leipzig, Germany Join Date: May 2012 Posts: 271	Upcoming workshop: A Beginner's Guide to RNA-Seq Data Analysis __________________ ecSeq Bioinformatics is Europe’s leading provider of hands-on bioinformatics workshops and professional data analysis in the field of Next-Generation Sequencing (NGS).