[maker-devel] Evidences in fasta format but be alignment in every run?

[Quanwei Zhang]

Great. Many thanks. So I can select part of my genome assembly for the
training. Which the following ways do you think is better? (a) Select the
longest contigs. (b) Randomly select contigs with any length?

Thank you!

Best
Quanwei

2017-02-10 11:39 GMT-05:00 Carson Holt <carsonhh at gmail.com>:

> MAKER is restartable. As long as you run each time in the same location,
> it can reuse existing alignments from the previous run. You also only need
> to train on ~10MB of the genome depending on gene density. Target size
> should be 300-400 genes.
>
> If you follow this GMOD wiki, this is demonstrated (you can also watch
> video - link as top of page - to see it being done) —>
> http://weatherby.genetics.utah.edu/MAKER/wiki/index.php/
> MAKER_Tutorial_for_GMOD_Online_Training_2014#Training_
> ab_initio_Gene_Predictors
>
> —Carson
>
>
>
> On Feb 10, 2017, at 8:50 AM, Quanwei Zhang <qwzhang0601 at gmail.com> wrote:
>
> Hello:
>
> I am annotating a new genome using Maker. I have RNA-seq assembly and
> protein sequences (from other organisms) in fasta format. Since I need to
> train gene finders, so I have to run Maker several times. I think the
> aligning process between the transcript assembly (protein sequences) and
> the genome assembly may be time consuming. So I wonder whether I can save
> such alignment in the first run, and then make use of such alignment in the
> following runs?
>
> Thanks
>
> Best
> Quanwei
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