RNA-Seq without reference

[kenosaki]

Hi
Does anyone try transcriptome analysis of the organism of which reference genome is unknown?
The organism is plant, and have about 80 % similarity of Arabidopsis genes at nucleotide level.
Data type is SOLiD. I think the first step is de novo assembly of RNA, followed by the read mapping and estimation of gene expression.
I haven't tried RNA de novo assembly yet. Any suggestion ?

Ken

[steven]

Hi
Does anyone try transcriptome analysis of the organism of which reference genome is unknown?
The organism is plant, and have about 80 % similarity of Arabidopsis genes at nucleotide level.
Data type is SOLiD. I think the first step is de novo assembly of RNA, followed by the read mapping and estimation of gene expression.
I haven't tried RNA de novo assembly yet. Any suggestion ?

Ken

Yes: "without a reference" in the search bar above.
It gives you this page:

http://seqanswers.com/forums/search.php?searchid=378543

where for instance this thread seems to be relevant to your interest.
hope it helps.
s.

[kenosaki]

http://seqanswers.com/forums/search.php?searchid=378543
where for instance this thread seems to be relevant to your interest

yes, this thread helps a lot.

Thanks Steven

[shilp]

Hi
Does anyone try transcriptome analysis of the organism of which reference genome is unknown?
The organism is plant, and have about 80 % similarity of Arabidopsis genes at nucleotide level.
Data type is SOLiD. I think the first step is de novo assembly of RNA, followed by the read mapping and estimation of gene expression.
I haven't tried RNA de novo assembly yet. Any suggestion ?

Ken