unclear point about strands about sniffles HOT 4 CLOSED

Hi,
thanks for reaching out. The strands should help with the design of primers for the PCR based validation of the breakpoints/ SVs. In most cases INV are ++/-- . There are however sometimes some more complicated breakpoints that change this rule of thump. I will update the header.

Let me know if you have further questions.
Thanks
Fritz

from sniffles.

Hi Fritz

thanks for kindness reply.
So strands don't have any relation with reference genome's direction?
I have thought that strands informations are corresponding to direction which SV goes from a break point.
and in case of TRA, like fusion genes, I think there are 4 types of connections between two chromosomes.
I wrote 4 cases and I'd like to know which strands pair (++, --, +-, -+) is most suitable for each case.

Thanks
Harazono

from sniffles.

Yes they encode the direction away or coming to the breakpoint, but they do not exactly relate to the strand (reference) itself.
e.g. I cannot predict the strand (reference) of a heterozygous deletion.

I hope that makes sense.
Cheers
Fritz

from sniffles.

thank you !

from sniffles.