Question: Can I align the transcriptome data against the genome of closely related organism
1
gravatar for lakshmi.bioinformatics
5.1 years ago by
India
lakshmi.bioinformatics20 wrote:

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

I have done de nova 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  funcitonal genomics with the trasnscriptome annotated data

rna-seq assembly • 1.6k views
ADD COMMENTlink modified 5.1 years ago by Istvan Albert ♦♦ 81k • written 5.1 years ago by lakshmi.bioinformatics20
1
gravatar for Chris Evelo
5.1 years ago by
Chris Evelo10.0k
Maastricht, The Netherlands
Chris Evelo10.0k wrote:

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. 

ADD COMMENTlink written 5.1 years ago by Chris Evelo10.0k

+1 for alignment of unassembled reads.

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

http://www.biomedcentral.com/1471-2164/15/570/abstract

ADD REPLYlink written 5.1 years ago by Charles Warden7.2k
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