<html><head><meta http-equiv="Content-Type" content="text/html; charset=utf-8"></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; line-break: after-white-space;" class="">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. <div class=""><br class=""></div><div class="">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 —> <a href="https://wjidea.github.io/defusion/Introduction.html" class="">https://wjidea.github.io/defusion/Introduction.html</a></div><div class=""><div class=""><br class=""></div><div class="">—Carson<br class=""><div><br class=""><blockquote type="cite" class=""><div class="">On Apr 30, 2020, at 6:58 AM, Lior Glick <<a href="mailto:liorglic@mail.tau.ac.il" class="">liorglic@mail.tau.ac.il</a>> wrote:</div><br class="Apple-interchange-newline"><div class=""><div dir="rtl" class=""><div style="" dir="ltr" class="">Thanks Carson - your answer was very helpful.</div><div style="" dir="ltr" class="">Another question related to the lift-over process, if I may.</div><div style="" dir="ltr" class="">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 <a href="https://computationalbiologysite.wordpress.com/2013/07/11/maker-gff-cite-online/" class="">this helpful post</a>, 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?</div><div style="" dir="ltr" class="">Thank you!</div></div><br class=""><div class="gmail_quote"><div dir="rtl" class="gmail_attr">בתאריך יום ה׳, 23 באפר׳ 2020 ב-20:43 מאת Carson Holt <<a href="mailto:carsonhh@gmail.com" class="">carsonhh@gmail.com</a>>:<br class=""></div><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex">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.<br class="">
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—Carson<br class="">
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<br class="">
<br class="">
> On Apr 21, 2020, at 7:08 AM, Lior Glick <<a href="mailto:liorglic@mail.tau.ac.il" target="_blank" class="">liorglic@mail.tau.ac.il</a>> wrote:<br class="">
> <br class="">
> Hello,<br class="">
> 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.<br class="">
> 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.<br class="">
> 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).<br class="">
> Why is this happening? Are there some cutoffs that are not satisfied? If so, what are they and how can they be configured?<br class="">
> <br class="">
> Thanks,<br class="">
> Lior<br class="">
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</blockquote></div>
<span id="cid:f_k9mrudqt1"><fusion.png></span></div></blockquote></div><br class=""></div></div></body></html>