Workshops
QIIME2 analysis of bacterial 16s rRNA – applications close 2 August
Lead trainer
Ashley Dungan, School of Biosciences, The University of Melbourne
Who is the workshop for?
Researchers and students at The University of Melbourne and its affiliated institutes only (refer to ‘Members’ section) who are new to analysis of bacterial communities using16sRNA who have some command line experience.
How to apply…
The workshop is free but due to anticipated high demand, participation is subject to selection through an expression of interest process.
Opening – 12noon, 20 July 2021
Deadline – 5pm, Monday 2 August 2021
Sumissions will be reviewed by our training team and all applicants advised of the status of their application (successful, waiting list, unsuccessful) by Thursday 5 August 2021.
Requirements
This online, hands-on workshop will be conducted online using Zoom, Slack and a remote (cloud) computer. Attendees must supply their own charged laptop with access to the internet/wifi and with the following software preinstalled:
- Windows users: A terminal emulator such as PuTTY (free and open-source) will need to be downloaded.
- Software for file transfers between a local computer and remote server such as WinSCP or FileZilla.
- Mac users: No additional software needs to be installed for this workshop.
Knowledge/experience of the command line is a necessary for this workshop. It will be run on a Nectar Instance. You will be given an individual IP address and password to log on to using the SSH client tool on your own computer (Terminal on Mac or PuTTY on Windows) and navigate the directory structure and `scp` files from a remote computer to your local computer.
Workshop Outline
This workshop will give you an introduction to the QIIME2 analysis platform using 16S rRNA amplicon data from coral-associated bacteria. Topics covered include:
- importing, cleaning and quality control of the data
- taxonomic analysis
- building a phylogenetic tree
- basic visualisations and statistics.
Learning Objectives
By the end of the workshop you should be able to:
- take raw data from a sequencing facility and end with publication quality graphics and statistics
- answer the question “What is the influence of genotype (intrinsic) and environment (extrinsic) on anemone-associated bacterial communities?”
For further information, email bioinformatics-training@nullunimelb.edu.au.
Workshops
Introduction to Genome Browsers – online
Visualisation gives you answers to questions you didn’t know you had – Ben Schneiderman
Workshop Outline
This hands on tutorial on Genome Browsers will provide beginners with an introduction to both the UCSC Genome browser and IGV (Integrated Genome Viewer) using RNAseq gene expression data. Tools and public datasets will be used to illustrate how the expression of transcript variants can be investigated in different tissues and cell types using public data, including human RNAseq data from GTEX and mouse cell type RNAseq data from Tabula Muris, as viewed within the UCSC genome browser. A subset of aligned reads from the single cell RNAseq data Celltax study from the Allen Brain Atlas will also be downloaded from the SRA database and visualised in IGV.
The data and genes used in this workshop focus on gene expression data taken from the neuroscience domain, however the analysis tools and visualizations demonstrated in this workshop can be applied to many research areas.
Trainer
Vicky Perreau, Training Lead & Senior Bioinformatician, Melbourne Bioinformatics
Learning objectives
At the end of the workshop, you will be able to:
- understand gene model representations and identify differences between transcripts variants
- investigate tissue/cell type expression profiles for genes in mouse and human gene expression data
- know some basic files types used in Genome browsers
- download BAM files from SRA and view in IGV
- use the ‘Blat’ tool to locate genomic regions with similarity to a sequence of interest
- create custom interactive views with multiple datatypes to share with colleagues and generate images for publications.
Target audience
The workshop is aimed at bench researchers with no coding/programming skills who wish to learn how to utilise online data and resources to refine their biological research questions and discovery.
Eligibility
This free workshop is available to staff and students at The University of Melbourne and its affiliated institutes only (refer to ‘Members’ section).
Required:
This is a hands-on workshop delivered via Zoom and attendees must use their own computers with access to the internet/wifi. We will be interacting with the web-based UCSC genome browser platform and locally installed IGV. A mouse is recommended for selecting screen elements during the workshop. The following software must also be preinstalled:
- web browser (Firefox or Chrome recommended)
- IGV (Integrated Genome Viewer) (free)
- obtain a login to UCSC Genome browser (free)
- Zoom (recently updated Version)
If you require any further information, or if you have any access requirements in order to participate in this workshop, please email us.
Workshops
Variant calling using GATK4 command line workflow – applications close 16 August
Lead trainer
Khalid Mahmood, Melbourne Bioinformatics, The University of Melbourne
Who is the workshop for?
Researchers and students at The University of Melbourne and its affiliated institutes only (refer to ‘Members’ section) with some knowledge of variant calling with some command line experience.
How to apply…
The workshop is free but due to anticipated high demand, participation is subject to selection through an expression of interest process.
Deadline – 5pm, Monday 16 August 2021
Submissions will be reviewed by our training team and all applicants advised of the status of their application (successful, waiting list, unsuccessful) by Thursday 19 August 2021.
Requirements
Basic knowledge/experience of the command line is necessary for this workshop. You will need to be able to “ssh” into a remote machine, navigate the directory structure and “scp” files from a remote computer to your local computer.
This is a hands-on workshop held in a zoom meeting room and using command line tools installed on a cloud computer. Attendees must use their own laptop with access to the internet/wifi and the following software preinstalled to log onto the cloud computer:
- Windows users: A terminal emulator such as PuTTY (free and open-source) will need to be downloaded.
- Software for file transfers between a local computer and remote server such as WinSCP or FileZilla.
- Mac users: No additional software needs to be installed for this workshop.
Cloud computer
Zoom meeting room and command line tools installed on a cloud computer. This workshop will be run on a Nectar Instance. You will be given an individual IP address and password to log on to using the SSH client tool on your computer (Terminal on Mac or PuTTY on Windows).
Workshop Outline
This workshop aims to introduce participants to variant calling using command line applications. The material follows the GATK variant calling best practices workflow and provides an introduction to tools, datatypes and file formats associated with variant calling. The workshop will use a test llumina sequencing data to progress through the workflow from aligning sequencing reads to a reference genome before applying the GATK best practices workflow to call genetic variants (SNVs and Indels) in test data.
Tools used:
- BWA
- Samtools
- GATK4
- picard
- bcftools
- jigv.
Learning Objectives
During this training participants will:
- align reads to a reference genome
- call simple variants using the GATK best practices workflow
- be introduced to SAM/BAM and VCF file formats
- follow instructions to run command line applications.
For further information, email bioinformatics-training@nullunimelb.edu.au.
Workshops
RNA-seq: from reads to differentially expressed genes – applications close 7 Sep
Submit an application to join this hands on 2 day workshop in RNA-seq analysis.
About this workshop
RNA-seq is a popular method for simultaneously measuring and comparing the expression of tens of thousands of genes in multiple samples.
Attendees can expect to gain an understanding of approaches to and practical experience in: quality control of short reads, alignment, gene counts, data normalisation, differential expression and visualisation. Places are limited to encourage discussion and experienced RNA-seq and Galaxy trainers will be present to answer your questions.
The workshop materials are based on the following Galaxy training workshops:
This training workshop will be conducted using Galaxy. It is important that you are familiar with navigating the Galaxy platform as the workshop will not include introductory content on how to use the platform. Attendance at a previous Galaxy workshop or working through this material is sufficient for attendance.
Lead trainers
Ms Jessica Chung & Dr Tom Harrop (Melbourne Bioinformatics)
Learning objectives
By the end of the workshop you should be able to:
- perform quality control of short reads using FastQC
- map reads to a reference genome using HISAT
- determine the number of reads mapped across genes or exons
- normalise read counts to account for composition bias
- perform differential expression analysis
- visualise results using a variety of plots.
Who is the workshop for?
This free workshop is available to staff and students at The University of Melbourne and its affiliated institutes only (refer to ‘Members’ section). It is aimed at researchers who have, or will soon acquire, RNA-seq short read data that they need to analyse themselves.
Required:
This is a hands-on workshop is being delivered over Zoom and using the Galax Australia open web based platform for analysis of data so attendees must have their own laptop with access to the internet/wifi and should register for a Galaxy account using their institutional email address. No additional software needs to be installed for this workshop and no progamming experience is necessary.
How to apply…
The workshop is free but due to anticipated high demand, participation is subject to application with selection. Places are strictly limited to 30 participants.
Deadline for applications is 5pm, AEDT Tuesday 7 September 2021.
Applications will be reviewed by the organising committee and all applicants will be informed of the status of their application (successful, waiting list, unsuccessful) by 5pm, Friday 10 September 2021.
If you require any further information, please contact us at bioinformatics-training@nullunimelb.edu.au.