Bioinformatics Seminar
Time:
Venue: Na
18 October 2016
NaSuperTranscript: a reference for analysis and visualisation of the transcriptome
Nadia DavidsonMCRI Bioinformatics
Transcriptomes are tremendously diverse and highly dynamic. Visualising and analysing this complexity is a major challenge. Indeed ; for species where no reference is available ; current methods limit how the transcriptome can be explored. We have developed a simple but elegant solution to allow many more analytical approaches to be applied in non-model organisms. A single representation for each gene ; consisting of all the unique exonic sequence ; in transcriptional order can be built and used as a reference. We refer to this concept as a superTranscript and have developed software ; Lace ; to construct them from any set of transcripts ; including de novo assembled transcripts. I show how superTranscripts used in non-model organisms allows for the first time ; visualisation of read coverage across a gene ; detecting differential exon usage and variant calling. SuperTranscripts also benefit visualisation and differential splicing detection in model organisms and I will provide some examples. Finally ; I will demonstrate how a reference and de novo assembled transcriptome can be combined into a compact superTranscriptome ; allowing easy identification of novel transcribed sequence. Applied to chicken RNA-Seq ; we found conserved coding sequence in over 1000 genes that was missed in the reference genome.;Davis Auditorium;;;