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

[Andre M. <And...@cr...>]

Dear Matt,

Thank you for your quick reply.

The quality of the reference sequence from which I derived the cds is not an issue.

I have full length transcript cDNA sequences I aligned to a high quality genome assembly.  From the alignment coordinates and using the genome assembly as source, I derived high quality mRNA sequences I used as input for transdecoder.

Deep RNA-seq data confirms the full length nature of my cDNA sequences. At the locations where my full length transcripts align I also have Augustus gene models supported by RNA-seq data. The ORFs of the predicted gene models generally correspond to the ORFs of transdecoder, with the exception, that in many cases transdecoder ORFs start upstream of the Augustus start codon and not with an ATG (5prime_partial, ORFs).

Best regards
André

On 14 May 2014, at 21:44, Matthew MacManes <mat...@un...<mailto:mat...@un...>> wrote:

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<http://genomebio.org/>
Office: 189 Rudman Hall I Lab: 145 Rudman Hall


On Wed, May 14, 2014 at 2:44 PM, Andre Minoche <And...@cr...<mailto: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<http://seq.crg.es/>


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