Hi

I think it depends what your goal is. If you trust your gene models and you
are after comparing gene expression for the known genes then I think
skipping reads that map to UTR is fine. It should average out in any case
over all genes if UTR reads are excluded for all. However that being said
high coverage in UTR's could also regulate gene expression. (
http://jvi.asm.org/cgi/content/short/84/5/2629)

Also if the gene model is not trust worthy or you are looking for novel
transcripts then possibly ignoring UTR's could have negative effect.

It will be good to hear from others. Happy to be corrected.

-Abhi

On Wed, Jun 29, 2011 at 5:07 PM, Kunbin Qu <KQu@genomichealth.com> wrote:

> Hi,
>
> A question about counting reads to the known genes from a RNA-seq run.
> Should the reads falling into the UTRs be included to represent the
> expression of the genes, or they should be excluded? I contacted Illumina's
> tech support, was told the gene counts does not include UTR in their CASAVA
> pipeline. Any opinion? Thanks.
>
> -Kunbin
>
>
>
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