Question: Frame number in Oncofuse output
0
gravatar for henryvuong
4.8 years ago by
henryvuong760
USA
henryvuong760 wrote:

Hi, 

I applied Oncofuse to annotate fusion genes from DNA-seq and would like to determine if the fusion is in-frame or not. Oncofuse provided 5_FRAME (frame of translated 5'FPG), 3_FRAME (frame of translated 3'FPG) and FPG_FRAME_DIFFERENCE (difference in 5' and 3' FPG frames). Their values are 0, 1 and 2. May I ask what these values mean? How do I interpret the FPG_FRAME_DIFFERENCE? Thanks.

oncofuse fusion • 1.4k views
ADD COMMENTlink modified 4.8 years ago by mikhail.shugay3.3k • written 4.8 years ago by henryvuong760
1
gravatar for mikhail.shugay
4.8 years ago by
mikhail.shugay3.3k
Czech Republic, Brno, CEITEC
mikhail.shugay3.3k wrote:

Hello!

The 5'FRAME is the frame of 5' fusion partner gene sequence at the breakpoint, same for 3'FRAME. FPG_FRAME_DIFFERENCE is the frameshift once fusion partner genes are joined.

FPG_FRAME_DIFFERENCE = (5'FRAME + 3'FRAME) % 3

If the sum of 5'FRAME and 3'FRAME is a multiple of 3, then the frame difference is 0 and fusion is considered in-frame, other situations mean out-of-frame.

PS. Just in case, here is the main thread for questions related to Oncofuse: Oncofuse: Prediction Of Driver Gene Fusions From Ngs Data

ADD COMMENTlink modified 4.8 years ago • written 4.8 years ago by mikhail.shugay3.3k
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