[BioC] DEXSeq - too many exons in gene

[Steve Lianoglou]

Hi,

On Fri, Feb 7, 2014 at 7:12 AM, Alejandro Reyes <alejandro.reyes at embl.de> wrote:
> Hi Antonio,
>
> As an extra comment, the binning that we do in DEXSeq is not mandatory to
> use DEXSeq for testing for alternative exon usage. For example, DEXSeq can
> be also used introducing counts from exon-exon junction reads (as in tools
> like MISO) or a "union" model like the one you mentioned. Another example of
> a very creative use is the one from a paper by Steve
> (10.1101/gad.229328.113), where they adapted their counting bins to test
> specifically for alternative 3' UTR lengthening independent from changes in
> gene expression.

Alejandro: thanks for the kind words and virtual citation ;-) DEXSeq
was an instrumental part of our analysis and we were very fortunate to
see it early on in bioc (even before your publication), so thank you
for putting your work out there for all of us to benefit.

Antonio: if you're working on ApA (I'm gathering yes ;-) and you have
any Q's about our work, I'd be happy to chat about it offline.

-steve

-- 
Steve Lianoglou
Computational Biologist
Genentech