[maker-devel] transcript assembly of RNA-seq data

[Quanwei Zhang]

Hello:

I wonder which is the best way to make use of RNA-seq data for gene
annotation of a new genome assembly.
(1) De novo assembly without mapping to any genome assembly (like Trinity)?
(2) TopHat+Cufflink do mapping to the new genome assembly, that want to
annotate?
(3) TopHat+Cufflink do mapping to a close annotated genome (like mouse or
human)?

Thanks

Best
Quanwei
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