> 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
> 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
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