RNA-Seq Data Analysis Online Course
Making Sense of RNA-Seq Data
RNA-Seq is sequencing of steady state RNA in a given sample.RNA-Seq is used for 1. identifying allele specific gene expression 2. finding novel transcripts and isoforms and 3. differential gene expression. This training programme exposes participants to the available public domain tools and techniques for the analysis of RNA-Seq data and addresses complete analysis pipeline from mapping reads to differential expression and systems biology. Course delivery includes prerecorded webinars and the exercise labs.
Course Duration
Course will run for four weeks from 02.01.2012 to 29.01.2012.
Course Material
Course material will be delivered online for each week at the start of the week. Register at http://www.labindia-gpod.com or write to [email protected]
Registration
Send a copy of your biodata along with DD of Rs 5000/- in the name of Labindia Instruments Pvt. Ltd. payable at Thane to Co-ordinator, Labindia-GPOD, Swnand, Jivan Vihar Housing Society, SB Road, Pune or make online payment with debit/credit card using payment gateway.
1. Tools for mapping reads to reference genome or transcriptome
A. Webinar : Overview of available tools and techniques for mapping reads to reference genome
B. Lab Exercises: Mapping reads to reference genome using Bowtie
2. De novo assembly of Transcriptome
A. Webinar : Tools and algorithms for De novo transcriptome assembly
B. Lab exercise : Using MIRA for De novo assembly
3. Finding isoforms and novel transcripts
A. Webinar : Overview of tools available for finding novel transcripts and isoforms
B. Lab exercises: Use of TopHat and Cufflink for finding isoforms and novel transcripts
4. Summarising mapped reads
A. Webinar : Review of tools for summarising mapped data and performing QC
B. Lab exercises : R Bioconductor tools for summarising mapped reads and QC
5.Normalization and Differential Expression
A. Webinar : Review of tools and method for normalising and analysis of differential expression of RNA-Seq data
B. R and Bioconductor tools for differential expression analysis prefernce will be given to DESeq package.
6. Gene set and pathway enrichment
A. Webinar : Overview of tools for gene set and pathways enrichment
B. Lab exercises : Goseq, Gostat and DAVID tools for enrichment analysis of differentially expressed genes.
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