search

petercombs / MPRA_selection

0 stars 1 forks source link

BLAST can sometimes not return any hits in Rodents #6

Closed petercombs closed 5 years ago

petercombs commented 5 years ago

It looks like TCF7L2, possibly among many others, does not return any rodent hits. As an outgroup, it does have 3 species in Equus (caballus, asinus, and przewalski), and one species of bat. Given that I'm not testing any of the ancestors actually along the outgroup branches, this isn't a huge issue, but the ancestor_comparisons step does assume that there will be an outgroup species in the tree. One simple option could be to include more outgroup species—possibly not even remove any species as outgroups. I need to think and test.

petercombs commented 5 years ago

So I believe I now have this fixed. Rather than specifying rodents as the outgroup, I am automatically having the outgroup be the next nearest node in the tree that is not the ingroup. So for TCF7L2, since there are Equids but not rodents, it will use those as the outgroup.