search

openvax / topiary

Predict mutated T-cell epitopes from sequencing data
Apache License 2.0
27 stars 9 forks source link

Optionally use isovar to construct coding/protein sequence #62

Open iskandr opened 7 years ago

hammer commented 7 years ago

@iskandr doesn't varcode construct the coding/protein sequence?

iskandr commented 7 years ago

Currently it does (in Topiary) but you can use Isovar to mostly by-pass reliance on the reference and instead build the coding sequence from RNA reads.

iskandr commented 7 years ago

In Vaxrank I currently first filter by Varcode's predicted effects (so that the effect vs. the reference is something non-silent in the coding sequence) and then use isovar to get the exact coding sequence including nearby other variants.

iskandr commented 6 years ago

@julia326 How did you get vaxrank working? Do you think you could apply the same magic to topiary.readthedocs.io?