Galaxy is an open source, web-based platform for data intensive biomedical research.

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RNA-Seq in Galaxy

Tue 20 Mar 2018 10:00am1:00pm

Venue

Queensland Biosciences Precinct
Building #80
St Lucia
Room: 
QBP Multi Media Room 3.141

The workshop introduces the concept of differential gene expression analysis with nextGen sequencing data, or RNA-Seq, using Galaxy platform. Galaxy has a user friendly interface and does not require programming skills or knowledge of unix for data analysis. The workshop is aimed for new Galaxy users with little or no experience in genomics or analysis of high-throughput sequencing data. The participants will align RNA-Seq data to a reference genome, visualise alignments and identify differentially expressed genes.

The workshop program:
• Introduction: Local resources for genomic research.
• Common formats in NGS analysis: FASTQ, BAM, SAM, GTF/GFF.
• RNA-Seq in Galaxy: analysis of differential gene expression using high-throughput sequencing data. We will cover general data manipulation in Galaxy and dedicated tools such as tophat (gapped aligner for RNA-Seq reads) and Cufflinks package.
• Visualisation of genomic data.
• Galaxy workflow. The participants will create, modify and use a Galaxy workflow.
• Q&A time

Participants have to bring laptops with Wi-Fi that can be connected to eduroam.

Please install Integrative Genomics Viewer from Broad Institute

We will go through ‘RNA-Seq Differential Gene Expression: Basic Tutorial’ developed by the Genomics Virtual Lab. The participants are encouraged to print the tutorial manual for the workshop. On the GVL website gvl.org.au switch to LEARN section, select ‘RNA Seq’, select ‘Basic Galaxy Tutorial’ and switch to ‘Tuxedo Protocol Tutorial’. Hint: save it as pdf, and print the pdf.

The workshop is free, but registration is essential. 

Workshop presenter: Dr Igor Makunin