[BioC] HTSeq-Count

[Steve Lianoglou]

Hi Julia,

On Fri, Sep 5, 2014 at 7:41 AM, Julia [guest] <guest at bioconductor.org> wrote:
> Hi all,
> I am new to the field of seq and performed a RIP-Seq experiment using HTSeq count as counter.
> I get now the following (using union, but doesn´t look better for interesection_strict):
> __no_feature    1503377
> __ambiguous     490772
> __too_low_aQual 0
> __not_aligned   0
> __alignment_not_unique  5277314
>
> When I sum up counts for all genes, I get 3227845.
>
> The number for __no_feature, __ambiguous, __alignment_not_unique look very high.
>
> Does somebody have an idea for that?

While I haven't worked with RIP-seq data myself, I do have some
experience with HITS-CLIP and PAR-CLIP, which I believe are quite
similar (at least in principle) -- these experiments must incredibly
difficult to pull off, however, because I'd say most of these types of
datasets that came my way were notoriously/incredibly noisy.

This is just to say the problem you are seeing may not be an
informatics problem, and could (quite possibly) be an experimental
one.

-steve

-- 
Steve Lianoglou
Computational Biologist
Genentech