Rna-Seq : Check For Fusions With A Known Position

Question

[Nicolas Rosewick]

Hi,

I was thinking on how to check for fusion events with an known position using RNA-Seq data. I know that I have several fusion events at different position with a specific exon. I put a figure to explain easily. So there are three different fusion point (green, yellow and pink) with exon1 of the gene. I know the exon sequence but how to check for the fusion point ? I was thinking on first align locally the reads on the exon sequence, to extract these reads, to remove the part that align on the exon sequence and to align them against the whole genome to find the position of the different fusion. What do you think ?

Thanks

[Keith Callenberg]

It sounds like a reasonable plan. Were you able to implement this? Was it successful?

Answer 1

[Xtof]

Hi

You can try using the software CRAC (http://crac.gforge.inria.fr/). It is a mapping software specially designed for finding fusion. I saw it in a meeting last week and it seemed quite performant.

[Nicolas Rosewick]

Thanks I will try it. But the idea is not to look for genome-wide fusion events but only for fusion with this specifi exon ( I know that there are multiple fusion events with different genomic position (on other chromosomes)