Thanks Jeremy,
   I will do it before try the *de novo *assembly.

Luciano

On Fri, May 18, 2012 at 1:44 PM, Jeremy Goecks <jeremy.goe...@emory.edu>wrote:

> I find a lot of potential new genes (hundreds or thousands of reads
> aligning to regions where there is no gene annotation),
>
>
> This shouldn't be completely unexpected. High-coverage RNA-seq data is
> constantly revealing new exons/splicing/transcripts, even in well-annotated
> genomes.
>
> I also find new exons for some genes or exons with different sizes. I was
> thinking to do an *de novo* assembly to find new transcripts and genes,
> but I was wondering if there is something else I could do.
>
>
> My suggestion: do reference-guided assembly with Cufflinks; this will
> yield both existing and new transcripts.
>
> For example, maybe I could just extract those regions where thousands of
> reads align (new gene). I know that we can extract the sequence data for
> specific transcript, is it possible to extract reads for regions without
> annotation, only based in the number of reads aligned?
>
>
> You could subtract known genes from the Cufflinks assembly to get only
> novel transcripts.
>
> Best,
> J.
>
>
>
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