[BioC] HTSeq-Count

[Steve Lianoglou]

Hi Julia,

On Mon, Sep 8, 2014 at 10:10 AM, Pickl, Julia
<j.pickl at dkfz-heidelberg.de> wrote:
> Hi Steve,
>
> thank you very much for your help.
>
> Which tool for DE did you use?
> I used edger, however I´ve read that edgeR and DESeq2 might be overstringent for RIP-Seq (f.e. RIP-Seeker package Paper, Supplement).

At the time, we used DESeq. I was comparing differential binding of an
RBP to targets between conditions, though. It seems like you want to
look at one condition and ask what transcripts are being bound by a
RBP, though.

In my opinion, the differential binding question is more interesting
and biologically relevant -- and likely to give you "real" signal.
Again it's my opinion, but doing one experiment and asking where your
RBP binds in that experiment in isolation (even though you have done a
control run in the same cell type/condition) likely won't mean all
that much.

-steve

-- 
Steve Lianoglou
Computational Biologist
Genentech