Re: [Transdecoder-users] ORFs without ATG as start

[Matthew M. <mat...@un...>]

Andre,

Alternatively, this could be a metric of assembly quality (e.g.
http://journal.frontiersin.org/Journal/10.3389/fgene.2014.00013/abstract)
which may be a function of the input data. Can you tell us a little bit
about the type and quantity of data used in this assembly?

Matt

 __________________________________
*Matthew MacManes*, Ph.D.
University of New Hampshire  I  Assistant Professor
Department of Molecular, Cellular, & Biomedical Sciences
Durham, NH  03824
Phone: 603-862-4052  I  Twitter: @PeroMHC <https://twitter.com/PeroMHC>
Web: genomebio.org
Office: 189 Rudman Hall I Lab: 145 Rudman Hall


On Wed, May 14, 2014 at 2:44 PM, Andre Minoche <And...@cr...> wrote:

>
> Hi,
>
> First of all thanks for providing a tool to predict ORFs.
>
> I am surprised to see, that so many of my ORFs predicted with
> transdecoder do not start with ATG (5prime_partial, 650 out of 1807).
>
> To me it seems like a malfunction of the software.
>
> Is there an easy way to trim the ORFs to the nearest start codon?
>
> Thanks
> André
>
> --
> André Minoche, Postdoc
>
> Centre for Genomic Regulation (CRG)
> Doctor Aiguader, 88, 4th floor
> 08003 Barcelona
>
> http://seq.crg.es
>
>
>
> ------------------------------------------------------------------------------
> "Accelerate Dev Cycles with Automated Cross-Browser Testing - For FREE
> Instantly run your Selenium tests across 300+ browser/OS combos.
> Get unparalleled scalability from the best Selenium testing platform
> available
> Simple to use. Nothing to install. Get started now for free."
> http://p.sf.net/sfu/SauceLabs
> _______________________________________________
> Transdecoder-users mailing list
> Tra...@li...
> https://lists.sourceforge.net/lists/listinfo/transdecoder-users
>