I would like to ask for your opinions. I have a WGS data set of mouse with a transgene inserted into it at an unidentified location causing a specific unexpected phenotype.
We would like to identify the insertion position(s).
I was thinking about trying a de-novo sequencing (SOAPdenovo) but I'm not sure if this is the correct approach. By de-novo sequencing I was hoping of identifying the transcripts containing the insertion site (it is ~6.2mb in size) and identify where it was lodged into the genome (mouse as a reference organism).
Do you think this can be a good solution?
Can anyone recommend a better approach or tool for this kind of analysis?