[maker-devel] maker-devel post from avhoeck at sckcen.be requires approval

[Carson Holt]

Hi Arne,

The genes found by CEGMA are very short genes, so where those genes might be identifiable at least partially on shorter contigs other genes will be far longer.  So the 87% value you get from CEGMA is probably what you are going to be able to find (even partially) for the entire genome. Remember that gene size when you include the introns can actually be quite large, and gene predictors need flanking signals from the sequence several hundred bp upstream and downstream to make a prediction, so having a gene partially contained by a contig makes that gene un-annotatable for ab initio predictors. Unless the organism has a high gene density or very few introns, you usually won’t be able to find a gene on contigs smaller than ~10kb.

—Carson



> On Mar 12, 2015, at 10:38 AM
> 
> From: Van Hoeck Arne <avhoeck at SCKCEN.BE <mailto:avhoeck at SCKCEN.BE>>
> To: "maker-devel at yandell-lab.org <mailto:maker-devel at yandell-lab.org>" <maker-devel at yandell-lab.org <mailto:maker-devel at yandell-lab.org>>
> Subject: TACC lonestar and N50 value
> Date: March 12, 2015 at 10:38:42 AM MDT
> 
> 
> Dear MAKER developer,
> 
> We have a plant genome of about 450 Mbp with an N50 value of 20 kbp whereas only 3/4 (333 Mbp) are contigs longer than 10 kbp. CEGMA said that 87% of the genes were found, whereas 94 % were partial identified.  You said last time that contigs smaller than 10kbp are not ideal for annotating and preferable to throw them away. Does this mean that I lose all genes present in the small contigs? Or is there another way to annotate them? (is concatenating all the small contigs together with 500 N's between each contig an option?)
> 
> Besides, i could run succesfully Maker via iplant's atmoshpere. However, for my large genomes i registred myself at the TACC lonestar cluster but Dave C. replied that i won't be able to run on the TACC supercomputers without an allocation. He said that I need to contact my PI. With my loginID, i haven't any acces to the cluser via ssh since my permission was denied. Therefore, is it possible to use the TACC supercomputers to run MAKER?
> 
> Best regards
> Arne
> 
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> From: maker-devel-request at yandell-lab.org <mailto:maker-devel-request at yandell-lab.org>
> Date: March 12, 2015 at 10:38:50 AM MDT
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