In new genome, how is it decided which strand is forward/reverse?

Question

[michael.nagle]

Is there any particular convention to this or is it just a coin toss?

I'm still pretty new to bioinformatics and I'm assuming the decision of which strand is forward and reverse on each scaffold/chromosome is determined by software in some way. How is this decision made?

[Devon Ryan]

You'd be surprised how many things come down to coin tosses :)

[Jean-Karim Heriche]

Which is why science is doomed in some countries:
UK moves towards cashless society
Sweden leads the race to become cashless society

Answer 1

[John Marshall]

I once heard a rumour that the strand that "most" genes get transcribed from gets designated as the forward strand. However one of the previous answers when this has come up on Biostars before suggests that it's about 50%-50% so that most isn't going to work too well.

See also Forward And Reverse Strand Conventions and Conventions For Designating Forward And Reverse Strands for example.

Googling this question leads to various interesting reading including this short article, which notes:

In all human reference chromosomes, as for other eukaryotes, the plus (+) strand is defined as the strand with its 5' end at the tip of the short arm (Genome Reference Consortium, personal communication, March 27, 2012).

…which seems fairly definitive and supports the centromere location discussion in the latter previous thread. But as noted in that thread, historical accidents occur and this doesn't necessarily hold for various particular species…