Thanks Jeremy, I will do it before try the *de novo *assembly. Luciano
On Fri, May 18, 2012 at 1:44 PM, Jeremy Goecks <[email protected]>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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