didn't the BowTie guys play around with various methods and settle on
splitting up multimapping reads between the supportable transcripts?  I
could have sworn they offered some empirical evidence to justify the choice.

now I am going to have to go and look for where I saw this... %^$@$#%^


On Tue, Jul 3, 2012 at 5:28 AM, Kasper Daniel Hansen <
kasperdanielhansen@gmail.com> wrote:

> There are many ways of doing the counting, including variants you have
> not listed.
>
> To my knowledge, no-one has ever really investigated the "right' way
> to this.  There are many recommendations around (including mine), but
> no-one has really investigated this well.  But it can (does) matter.
>
> Kasper
>
> On Tue, Jul 3, 2012 at 8:06 AM, Cittaro Davide <cittaro.davide@hsr.it>
> wrote:
> > Hi all, just a quick question on best practices to create datasets for
> RNA-seq analysis with edgeR or limma:::voom().
> > I must create a table in which read counts for every entity (i.e. every
> transcript) for every sample. In order to do this I have at least a couple
> of options that may affect results:
> > 1- should I count all reads overlapping the whole transcript or the
> reads that overlap exons?
> > 2- should I use every transcript or just the primary one?
> >
> > Thanks
> >
> > d
> >
> > /*
> > Davide Cittaro, PhD
> >
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> > Center for Translational Genomics and Bioinformatics
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> > 20132 Milano
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> >
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> > Mail: cittaro.davide@hsr.it
> > Skype: daweonline
> > */
> >
> >
> >
> >
> >
> >
> >
> >
> >
> >
> >
> >
> >
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-- 
*A model is a lie that helps you see the truth.*
*
*
Howard Skipper<http://cancerres.aacrjournals.org/content/31/9/1173.full.pdf>

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