dear Simon,

thanks for your reply, now its more clear what is happening. My issue was
that even discarding the reads of the gene fusions, the total of counts of
the exons was still much higher that the total number of reads aligned, now
I understand from your reply and Steven that this will occurs when reads
overlap 2 exons of the same gene, and then this explains the multiplication
of reads that we observe. We will disregard the counts of gene fusions.

Kind regards,

Andreia



On Thu, Jun 27, 2013 at 10:01 AM, Simon Anders <anders@embl.de> wrote:

> Hi,
>
> I'm not sure if I completely understand what the question is, but maybe
> the following remarks help:
>
> If a read overlaps with several exons of the _same_ gene, dexseq_count.py
> counts the read for each of these exons. If the read overlaps with exons
> from different genes, it gets discarded.
>
> Unfortunately, annotation files such as Ensembl's GTF file for humans,
> have a few overlapping genes: The right-most exons of one gene overlap or
> are even identical with the lef-most exons of the neighboring gene.
> According to the rules just stated, reads mapping to these exons should get
> discarded, because we would not be able anyway to say which of the two gene
> to count this for.
>
> One might, however, also argue that if an exon is assigned to two genes
> then these are not two genes, but different sets of isoforms of one and the
> same gene. Therefore, dexseq_prepare_annotation.py will "fuse" these genes
> into an "aggregate gene" and give it a name formed by concatenating the
> fused genes' names with plus signs.
>
> This sounded good in theory but, in practice, turned out to be not that
> useful, because such aggregate genes are hard to interpret. Furthermore,
> the Ensembl curators probably had good reasons to not fuse the two genes,
> and the better strategy might hence be to keep the genes seperate and
> accept that we cannot do inference on the one or two exons that overlap
> between he genes.
>
> Hence, the new version of dexseq_prepare_annotation.py now accepts a new
> option, '-r', which switches off gene aggregation ('-r no').
>
>   Simon
>



-- 
---------------------------------------------------------------------------------------------
Andreia J. Amaral, PhD
BioFIG - Center for Biodiversity, Functional and Integrative Genomics
Instituto de Medicina Molecular
University of Lisbon
Tel: +352 217500000 (ext. office: 28253)
email:andreiaamaral@fm.ul.pt ; andreiaamaral@fc.ul.pt

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