Fusion gene detection - case and control samples

Question

[ninninahm]

HI all!

My goal is to detect fusion genes in my case samples that are not in my control samples.

For this, I want to use the tool FusionCatcher to detect fusion genes in my data. I have 10 control samples and 20 case samples in mouse. In the tool you can specify an extra input folder for normal data, however, my data is not matching, they are 30 individual mice. Does it make sense to use the matching control option or can I use it for any control?

fusioncatcher.py -d mouse_build -i mouse_cases -I mouse_ctrl -o results -p 5

mouse_cases contains paired end fastq data from the case samples

mouse_ctrl contains paired end fastq data from the control samples

My question is: Can I do it like this or should I run FusionCatcher twice with the respective input folder and no ctrl folder?

Thank you for your help!

Nina