H3ABioNet

Pan African Bioinformatics Network for H3Africa

Measurement and analysis of mRNAs and long non-coding RNAs using next generation sequencing (RNASeq)


These one day courses are designed for scientists and clinicians with little or no experience in next generation sequencing. The courses aim to provide the experimental and bioinformatics skills required to prepare samples, quantify the levels of mRNA/long-non-coding RNA (RNAseq) or exon/DNA (DNAseq) expresion. We assume that sequencing will be performed by an external provider and will provide advice in this area. The courses are computer based and will involve a combination of presentations/exercises to analysis 'actual' next generation sequencing data using publically (free) available programmes.
Content:

  • Overview on mRNAs and long non-coding RNAs
  • Introduction to RNA databases (Ensembl, RefSeq, GenBank and human lincRNA catalogue)
  • RNA isolation techniques and quality assessment
  • Overview of next generation sequencing platforms (ABI Solid, Illumina Solexa, Life Technologies Ion Torrent)
  • Introduction to data file formats (FASTA, FASTQ, SAM, BAM, GTF and BED files)
  • Mapping of RNA data onto a reference genome using Tophat
  • Quantification of known RNA species using CuffDiff
  • Identification and quantification of novel RNA transcripts using CuffLinks
  • Visualisation and analysis of sequencing data using the IGV genome browsers
  • Functional annotation using DAVID pathway analysis

Course Trainers: Dr Nick Ilott (University of Oxford) and Prof Mark Lindsay (University of Bath)
Dates and location:
Tuesday 9th July 2013 - IMG Training Rooms, Near Liverpool Street Station, London