I try to use TopHat for RNA-seq data. The Culex quinquefasciatus genome will be used for the TopHat. Would you me a guide which genome data that I need to use along with RNA-seq data (from Illumina HighSeq)?
Here is the Culex quinquefasciatus genome data webpage. https://www.vectorbase.org/organisms/culex-quinquefasciatus
Assembly, Gene set, Scaffolds?