Can I align the transcriptome data against the genome of closely related organism

Question

[lakshmi.bioinformatics]

I have got the transcriptome of an organism whose genome has not yet been sequenced

I have done de novo assembly and annotation using online servers

How to check if the quality of assembly and annotation is good?

Can I align the transcriptome data against the genome of closely related organism

Is it good to perform functional genomics with the trasnscriptome annotated data

Answer 1

[Chris Evelo]

Yes, you can align the transcriptome data against the genome of a closely related organism. You could in fact do that with the unassembled data and that should help you a lot with your other questions.

[Charles Warden]

+1 for alignment of unassembled reads.

For example, here is a paper describing such an application for a non-human primate.