[BioC] HTSeq-Count

Steve Lianoglou lianoglou.steve at gene.com
Fri Sep 5 18:35:10 CEST 2014

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


Steve Lianoglou
Computational Biologist

More information about the Bioconductor mailing list