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Hi,<br>
<br>
Thank you for your answer.To get my gff with ab-initio predictions,
I just took the corresponding lines in the maker gff from the
previous round.<br>
<br>
I can't see any problem with it, it looks like this:<br>
<br>
<font size="-2">Plvit001 augustus_masked match 66626
70338 0.85 + .
ID=Plvit001:hit:12095:4.5.0.0;Name=augustus_masked-Plvit001-abinit-gene-0.7-mRNA-1<br>
Plvit001 augustus_masked match_part 66626 67586
0.85 + .
ID=Plvit001:hsp:27621:4.5.0.0;Parent=Plvit001:hit:12095:4.5.0.0;Target=augustus_masked-Plvit001-abinit-gene-0.7-mRNA-1
1 961 +;Gap=M961<br>
Plvit001 augustus match 66626 70338 1
+ .
ID=Plvit001:hit:12088:4.5.0.0;Name=augustus-Plvit001-abinit-gene-0.0-mRNA-1<br>
Plvit001 augustus match_part 66626 70096
1 + .
ID=Plvit001:hsp:27610:4.5.0.0;Parent=Plvit001:hit:12088:4.5.0.0;Target=augustus-Plvit001-abinit-gene-0.0-mRNA-1
1 3471 +;Gap=M3471<br>
Plvit001 augustus_masked match_part 68166 68486
0.85 + .
ID=Plvit001:hsp:27622:4.5.0.0;Parent=Plvit001:hit:12095:4.5.0.0;Target=augustus_masked-Plvit001-abinit-gene-0.7-mRNA-1
962 1282 +;Gap=M321<br>
Plvit001 augustus_masked match_part 69504 70096
0.85 + .
ID=Plvit001:hsp:27623:4.5.0.0;Parent=Plvit001:hit:12095:4.5.0.0;Target=augustus_masked-Plvit001-abinit-gene-0.7-mRNA-1
1283 1875 +;Gap=M593<br>
Plvit001 augustus_masked match_part 70174 70338
0.85 + .
ID=Plvit001:hsp:27624:4.5.0.0;Parent=Plvit001:hit:12095:4.5.0.0;Target=augustus_masked-Plvit001-abinit-gene-0.7-mRNA-1
1876 2040 +;Gap=M165<br>
<br>
</font><br>
Best regards,<br>
<br>
Yann<br>
<br>
<div class="moz-cite-prefix">On 09/03/2017 18:52, Carson Holt wrote:<br>
</div>
<blockquote
cite="mid:E18ED5CD-A2B4-4E72-AE63-71EC4FCB6D65@gmail.com"
type="cite">
<pre wrap="">My guess is that there is either an issue with the GFF3 file you supplied, so its features are not overlapping anything.
—Carson
</pre>
<blockquote type="cite">
<pre wrap="">On Mar 6, 2017, at 9:51 AM, YannDussert <a class="moz-txt-link-rfc2396E" href="mailto:dussert.yann@gmail.com"><dussert.yann@gmail.com></a> wrote:
Hello,
First, thank you for developing MAKER, this is a great annotation tool!
I am trying to annotate the genome of a biotrophic oomycete with MAKER. After reading multiple posts on this list, I first used RNA-seq data and a protein set from other oomycetes to create a first training set. I then used augustus, snap (both trained with models from the first round) and genemark for ab-initio gene prediction during a second round (masked and unmasked genome). I ran MAKER with the following options: single_exon=1, split_hit=5000, correct_est_fusion=1.
After the second round, I had only around 11000 annotated genes (96% completeness with Busco V2), whereas I'm expecting between 13000-17000 genes (numbers from other annotated oomycetes). There was only around 1500 genes in the non_overlapping protein file. After looking at the annotation on a genome browser, one of the problems was apparently gene fusions due to bad protein evidence. Following the advice on another post, I tried running MAKER by passing the ab-initio predictions with pred_gff, to avoid using bad protein hints for gene predictors. I still have around 11000 annotated genes, but now there are 10000 genes in the non_overlapping protein file. Why this difference? I thought that this file included gene predictions not supported by any evidence, did I miss something?
Thank you in advance for your answer.
Best regards,
Yann
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</pre>
</blockquote>
<pre wrap="">
</pre>
</blockquote>
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