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 <[email protected]> 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 > > > > ______________________________________________________________________ > The contents of this electronic message, including any attachments, are > intended only for the use of the individual or entity to which they are > addressed and may contain confidential information. If you are not the > intended recipient, you are hereby notified that any use, dissemination, > distribution, or copying of this message or any attachment is strictly > prohibited. If you have received this transmission in error, please send an > e-mail to [email protected] and delete this message, along with > any attachments, from your computer. > [[alternative HTML version deleted]] > > _______________________________________________ > Bioc-sig-sequencing mailing list > [email protected] > https://stat.ethz.ch/mailman/listinfo/bioc-sig-sequencing > [[alternative HTML version deleted]] _______________________________________________ Bioc-sig-sequencing mailing list [email protected] https://stat.ethz.ch/mailman/listinfo/bioc-sig-sequencing
