[maker-devel] Missing genes in lift-over with est2genome

[Carson Holt]

If using the est_forward=1 options for the leftover, you can also anchor a search to a specific contig or region by adding a tag to the fasta header (  maker_coor=contig:1-1000; ). The tag will force Exonerate to only run on that region. Sometimes that can rescue a model. 

When you pass results into model_gff=, it will leave them unchanged. It just accepts or rejects them as is. But the model itself is considered evidence, and can alter clustering.  Other_gff= just passes things through with no processing or evaluation (it’s like cut and paste).  You can also try deFusion on result models for resolving gene fusions —> https://wjidea.github.io/defusion/Introduction.html <https://wjidea.github.io/defusion/Introduction.html>

—Carson

> On Apr 30, 2020, at 6:58 AM, Lior Glick <liorglic at mail.tau.ac.il> wrote:
> 
> Thanks Carson - your answer was very helpful.
> Another question related to the lift-over process, if I may.
> I want to take the resulting gff and pass it on to another MAKER run, where I provide further, lower confidence evidence (ESTs and proteins). I'm not sure which option to use though. According to this helpful post <https://computationalbiologysite.wordpress.com/2013/07/11/maker-gff-cite-online/>, I tried using pred_gff and model_gff, but both created cases of fusion genes when genes are very adjacent to one another (see attached picture), even with the correct_est_fusion parameter enabled. It looks like the only way to take lifted-over genes "as-is" would be to use other_gff, but I figure that this was not really intended for genes. Would you recommend this usage? Am I missing something?
> Thank you!
> 
> ‫בתאריך יום ה׳, 23 באפר׳ 2020 ב-20:43 מאת ‪Carson Holt‬‏ <‪carsonhh at gmail.com <mailto:carsonhh at gmail.com>‬‏>:‬
> There are percent cutoffs for the est2genome algorithm you can set in the maker_bopts.ctl file. Additionally, maker will give the alignment but not produce a gene model if it can’t translate through the est2genome alignment (i.e. stop codons in the assembly). I believe the cutoff is 50%. If you add est_forward=1 to the maker_opts.ctl file names will be copied from the alignment source and the score in the GFF3 column will be the percent match to the original transcript.
> 
> —Carson
> 
> 
> 
> > On Apr 21, 2020, at 7:08 AM, Lior Glick <liorglic at mail.tau.ac.il <mailto:liorglic at mail.tau.ac.il>> wrote:
> > 
> > Hello,
> > I am using MAKER to annotate a plant genome assembly. A high-quality reference genome and annotation exists for another variety of the same species, so my first step is lifting over reference genes to my genome. I do this by setting est2genome = 1 and providing MAKER with the reference cDNA (transcriptome). No other evidence is provided and no prediction is performed. Repeat masking is done using the reference repeats library.
> > When checking the results, I found out lots of reference genes missing from the lift-over result. However, if I blast the sequences of these genes myself, I get good matches. I even see these matches when I look at the blast results buried in the MAKER data_store.
> > For example, a transcript of length 1077 got a match of length 855 - 100% identity and no gaps. Bitscore was 1709 and E-value 0. This looks like a pretty good match, but it is not found in the final MAKER results (gff/fasta).
> > Why is this happening? Are there some cutoffs that are not satisfied? If so, what are they and how can they be configured?
> > 
> > Thanks,
> > Lior
> > _______________________________________________
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> 
> <fusion.png>

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