> 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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