I have been reading "FACTERA : a practical method for the discovery of genomic rearrangements at breakpoint resolution".
While reading this paper, there is a explanation about its process.
anyway, In this paper, soft-clipping with orientation concept is hard to understand. So I am appreciated if you look at it.
Four orientation of R1 and R2 are possible.(Fig.1D).However, only cases 1a and 2a shown in Figure !d can generate valid fusions, as their reads have soft-clipped sequences facing opposite directions. Thus , before k-mer comparison (Fig.1C), the reverse complement of R1 is taken for cases 1b and 2b, respectively, converting them into cases 1a and 2a.
In this paragraph, I can confirm the 1a 2a has the opposite directions in soft-clipped reads, but why only fusion is to be opposite direction in soft-clipped. I can't understand.
Can anyone help me understand this further more with picture?