Hey there,
I am currently analysing a somewhat doubtful fusion call and I found 9 supporting read pairs for the call. Based on UMIs they all originate from both strands of a single molecule. So given this evidence, I am reasonably confident that there was such a molecule in the library, however, when sequencing the same sample again much deeper, we could not find any evidence for this event.
The evidence for the fusion is also somehow indirect, as the R1 reads and the R2 reads do not overlap at all, which is very rare given the fragment size distribution we generally see.
My hypothesis is that this molecule arose as an artefact during library preparation. I could imaging that during fragmentation or at a similar step such chimeric molecules may be created, but I don't know how frequent that is or which specific steps give rise to such artefacts. If someone has experience with that, that would be super helpful.
Thanks for your help,
Jonas
I am currently analysing a somewhat doubtful fusion call and I found 9 supporting read pairs for the call. Based on UMIs they all originate from both strands of a single molecule. So given this evidence, I am reasonably confident that there was such a molecule in the library, however, when sequencing the same sample again much deeper, we could not find any evidence for this event.
The evidence for the fusion is also somehow indirect, as the R1 reads and the R2 reads do not overlap at all, which is very rare given the fragment size distribution we generally see.
My hypothesis is that this molecule arose as an artefact during library preparation. I could imaging that during fragmentation or at a similar step such chimeric molecules may be created, but I don't know how frequent that is or which specific steps give rise to such artefacts. If someone has experience with that, that would be super helpful.
Thanks for your help,
Jonas