de novo assembly vs. mapping for splice variant or fusion transcript detection

[onconaut]

Hello everyone, I am new to the sequencing world and just joined this forum.

We would like to do whole transcriptome sequencing on human tissue in order to identify (new) splice variants and fusion transcripts to see how they are associated with outcome in a particular cancer.

I have seen there are different approaches using either mapping to a reference genome or de novo assembly.
What is the advantage of using the de novo assembly strategy?
Given the requirements for computational power is it worth going the de novo assembly route?

Thanks for your input,
O.

[DZhang]

Hi Onconaut,

If your fusion genes and splice variants are complex, de novo approach is worth trying. However, you still need to filter properly mapped reads initially. You may check a few publications on fusion gene identification.

Best regards,
Douglas

https://www.contigexpress.com

[ndaniel]

Have you tried FusionCatcher for finding fusion genes in RNA-seq data?

FusionCatcher has been used for finding novel and known fusion genes (and their alternative splicing events) in the following articles:
- S. Kangaspeska, S. Hultsch, H. Edgren, D. Nicorici, A. Murumägi, O.P. Kallioniemi, Reanalysis of RNA-sequencing data reveals several additional fusion genes with multiple isoforms, PLOS One, Oct. 2012. http://dx.plos.org/10.1371/journal.pone.0048745
- H. Edgren, A. Murumagi, S. Kangaspeska, D. Nicorici, V. Hongisto, K. Kleivi, I.H. Rye, S. Nyberg, M. Wolf, A.L. Borresen-Dale, O.P. Kallioniemi, Identification of fusion genes in breast cancer by paired-end RNA-sequencing, Genome Biology, Vol. 12, Jan. 2011. http://genomebiology.com/2011/12/1/R6