Question: Rna-Seq : Check For Fusions With A Known Position
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gravatar for Nicolas Rosewick
6.8 years ago by
Belgium, Brussels
Nicolas Rosewick8.8k wrote:

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

enter image description here

fusion rna-seq • 2.1k views
ADD COMMENTlink modified 6.8 years ago by Xtof170 • written 6.8 years ago by Nicolas Rosewick8.8k

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

ADD REPLYlink written 5.1 years ago by Keith Callenberg900
0
gravatar for Xtof
6.8 years ago by
Xtof170
Paris
Xtof170 wrote:

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.

ADD COMMENTlink written 6.8 years ago by Xtof170

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)

ADD REPLYlink written 6.8 years ago by Nicolas Rosewick8.8k
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