[BioC] Counting reads for edgeR or voom()

[Kasper Daniel Hansen]

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 at 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
>
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