CGEBM Training Workshops 2015/16
All workshops will be held in the MacRobert Building Computer Suite MR117.
The introductory lecture takes place in the IMS Level 7 Conference Room.
*The introductory lecture and the first three workshops are essential
prerequisites for ALL of the other courses. Please make every effort to attend
these if you plan on attending further workshops. If you have previous
experience in these topics please contact Sophie Shaw (s.shaw@abdn.ac.uk) and
she will advise on which prerequisite workshops will be best to attend.
Workshop
Introductory Lecture*
Date/Location
Lead Instructor
th
Wednesday 7 October
Brennan Martin
9-11 am
FH IMS Level 7 Conference
Room
Topics covered include sequencing technologies, types of genomics experiments,
and experimental considerations.
Crash Course for PIs
Wednesday 7th October
CGEBM Team
9-11 am
FH IMS Level 7 Conference
Room
An overview of suitable tools, output data format, quality checks and
experimental considerations. Designed for Principal Investigators so that they
can aid their researchers during genomics research.
Intro to The Computing
Wednesday 21st October
Sophie Shaw
Cluster – Maxwell and
2-5 pm
Unix Basic Skills*
Unix Basic Skills Contd*
Wednesday 28th October
Sophie Shaw
2-5 pm
Topics include an introduction to Maxwell, an introduction to Unix, file
hierarchy, navigating the system, binary programs, basic handling of genomics
data and pipelines.
Unix Basics and How to
Monday 2nd November
Sophie Shaw
Use Maxwell*
9-12 am
Continuation of Unix commands, shell scripts, using Maxwell to submit a job, and
monitoring job progress.
Advanced Unix and
Monday 2nd November
Sophie Shaw
Maxwell
2-5 pm
More advanced Unix commands including regular expressions, sed and loops.
Advanced Maxwell job submission such as submitting multiple jobs at once.
Genome Assembly and
Tuesday 1st December
CGEBM Team
Annotation using Galaxy
9 am-12.30 noon
Genome Assembly and
Tuesday 1st December
CGEBM Team
Annotation using the
1.30-5 pm
Command Line
Participants will take DNA sequencing data, run quality control, carry out de
novo assembly, and assess assembly metrics and presence of contamination.
Galaxy will demonstrate this workflow through an interactive user interface
whereas the command line will demonstrate the individual steps and parameter
choices.
Molecular Phylogenetics
Monday 25th January
Matthew Gemmell
9 am-5 pm
An introductory session to the concepts and uses of molecular phylogenetics.
This will involve sequence alignment, genetic distance calculation methods,
phylogenetic tree production and assessment of calculated phylogenies. The
molecular phylogenetic program MEGA will be introduced and taught concepts
will be put into practice through various examples and exercises. This course is a
good pre-cursor to the Mothur workshop; therefore individuals planning to
attend that workshop are advised to attend this workshop.
RNA sequencing and
Monday 1st Februrary
CGEBM Team
Differential Expression
9 am-12.30 noon
using Galaxy
RNA sequencing and
Monday 1st Februrary
CGEBM Team
Differential Expression
1.30-5 pm
using the Command Line
Participants will take RNA sequencing data, run quality control, align reads to a
reference genome, quantify reads at genes, identify differentially expressed
genes and explore tools for visualisation. Galaxy will demonstrate this workflow
through an interactive user interface whereas the command line will
demonstrate the individual steps and parameter choices.
Microbial Community
Monday 22nd February &
Alan Walker &
Analysis with Mothur and
Tuesday 23rd February
Matthew Gemmell
Visualisation using R
9 am-5 pm
Use of the software mothur to take 16S rRNA gene amplicon DNA sequences and
analyse the diversity and composition of bacterial communities. The command
line will be used to quality control sequences, cluster these into taxa and produce
diversity measures. Web apps & basic R scripting will be used to visualise
mothur output.
Alignment, Visualisation
Wednesday 2nd March
CGEBM Team
and Variant Calling using
9 am-12.30 noon
Galaxy
Alignment, Visualisation
Wednesday 2nd March
CGEBM Team
and Variant Calling using
1.30-5 pm
the Command Line
Participants will take DNA sequencing data, run quality control, align reads to a
reference genome, visualise alignments and identify regions containing
polymorphisms. Galaxy will demonstrate this workflow through an interactive
user interface whereas the command line will demonstrate the individual steps
and parameter choices.
Chip Seq Analysis
Wednesday 27th April
Eduardo De paiva
9 am- 5pm
Alves
An introduction into chromatin-immunoprecipation sequencing and how this
data can be used to identify regions bound by transcription factors. Analysis of
Chip-Seq data will be undertaken using the interactive Galaxy user interface.
Further Training in Next
Tuesday 31st May
Sophie Shaw
Generation Sequencing
9 am- 5pm
Analysis (TBC)
This session is currently free to carry out training in other areas yet to be
covered. If you have a topic that you think would be suitable, get in touch.