[maker-devel] Gene loss in subsequent round of maker for fungal genome annotation
Carson Holt
carsonhh at gmail.com
Fri Mar 23 11:28:50 MDT 2018
Run A —> no gene prediction, just cut and paste of transcript/protein alignments to generate rough models.
Run B —> Gene predictions based on training using only highly conserved subset of genes (you will have low sensitivity)
Run C —> Gene predictions based on training using broader gene set. Higher sensitivity but potentially lower specificity (sensitivity gains should outweigh any specificity loss).
Finally, mnake sure you look at models in a browser to see how well evidence and models overlap. If gene fusion is an issue (falsely merged mRNA-seq assembly results will generate hints that can cause gene predictors to fuse gene models), try deFusion —> https://wjidea.github.io/defusion/installation.html
—Carson
> On Mar 21, 2018, at 3:05 AM, Urmi <urmi208 at gmail.com> wrote:
>
> Hello maker community,
>
> I am trying to run maker 3.01.02-beta on a fungal genome. I am using available EST and protein sequences from a different strain of the same species using parameters "est" and "protein" in the maker_opts.ctl file. Here is the protocol I am using:
>
> Run maker with repeat masking and providing transcript and protein sequences from related species (Run A)
> Create SNAP model with CEGMA
> Train Augustus with BUSCO
> Run (run B ) with the new SNAP (done at step 2) and augustus species with options turned off (est2genome=0) and (protein2genome=0) data, provide gff file (altest_gff=runA_cdna2genome.gff, protein_gff=runA_protein2genome.gff3)
> Create SNAP model from run B.
> Train Augustus with transcripts from run B and BUSCO
> Run (run C ) with the new SNAP (done at step 5) and augustus species with options turned off (est2genome=0) and (protein2genome=0) data, provide gff file (altest_gff=runA_cdna2genome.gff, protein_gff=runA_protein2genome.gff3), keep_preds=1
> As a result of this, I get following gene numbers:
>
> run A: 12796 total genes out of which 12771 have AED < 0.5
> run B:10713 total genes out of which 10701 have AED < 0.5
> run C: 12651 total genes out of which 12582 have AED < 0.5
> Looking at the gff files in detail, it is observerd that there are some gene models in run A which are lost in run B and gain in run C. I don't understand why there is gene loss for run B. Here is an example:
>
> RunA
>
> contig1 maker gene 20468 21193 . + . ID=maker-contig1-exonerate_protein2genome-gene-0.34;Name=maker-contig1-exonerate_protein2genome-gene-0.34
> contig1 maker mRNA 20468 21193 100 + . ID=maker-contig1-exonerate_protein2genome-gene-0.34-mRNA-1;Parent=maker-contig1-exonerate_protein2genome-gene-0.34;Name=maker-contig1-exonerate_protein2genome-gene-0.34-mRNA-1;_AED=0.30;_eAED=0.30;_QI=0|-1|0|1|-1|0|1|0|241
> contig1 maker exon 20468 21193 . + . ID=maker-contig1-exonerate_protein2genome-gene-0.34-mRNA-1:1;Parent=maker-contig1-exonerate_protein2genome-gene-0.34-mRNA-1
> contig1 maker CDS 20468 21193 . + 0 ID=maker-contig1-exonerate_protein2genome-gene-0.34-mRNA-1:cds;Parent=maker-contig1-exonerate_protein2genome-gene-0.34-mRNA-1
> contig1 blastn expressed_sequence_match 20468 21193 726 + . ID=contig1:hit:983:3.2.0.0;Name=jgi|test_1|140804|est target_length=726
> contig1 blastn match_part 20468 21193 726 + . ID=contig1:hsp:998:3.2.0.0;Parent=contig1:hit:983:3.2.0.0;Target=jgi|test_1|140804|est 1 726 +;Gap=M726
> contig1 est2genome expressed_sequence_match 20468 21193 3630 + . ID=contig1:hit:1022:3.2.0.0;Name=jgi|test_1|140804|est;target_length=726;aligned_coverage=100;aligned_identity=100
> contig1 est2genome match_part 20468 21193 3630 + . ID=contig1:hsp:1110:3.2.0.0;Parent=contig1:hit:1022:3.2.0.0;Target=jgi|test_1|140804|est 1 726 +;Gap=M726
>
> RunB:
> contig1 est_gff:est2genome expressed_sequence_match 20468 21193 3630 + . ID=contig1:hit:1051:3.12.0.0;Name=jgi|test_1|140804|est;target_length=726;aligned_coverage=100;aligned_identity=100;aligned_coverage=100;aligned_identity=100;score=3630;target_length=726
> contig1 est_gff:est2genome match_part 20468 21193 3630 + . ID=contig1:hsp:1166:3.12.0.0;Parent=contig1:hit:1051:3.12.0.0;Target=jgi|test_1|140804|est 1 726 +;Gap=M726
>
> RunC:
> contig1 maker gene 20468 21193 . + . ID=snap_masked-contig1-processed-gene-0.5;Name=snap_masked-contig1-processed-gene-0.5
> contig1 maker mRNA 20468 21193 . + . ID=snap_masked-contig1-processed-gene-0.5-mRNA-1;Parent=snap_masked-contig1-processed-gene-0.5;Name=snap_masked-contig1-processed-gene-0.5-mRNA-1;_AED=0.30;_eAED=0.30;_QI=0|-1|0|1|-1|1|1|0|241;_merge_warning=1
> contig1 maker exon 20468 21193 . + . ID=snap_masked-contig1-processed-gene-0.5-mRNA-1:1;Parent=snap_masked-contig1-processed-gene-0.5-mRNA-1
> contig1 maker CDS 20468 21193 . + 0 ID=snap_masked-contig1-processed-gene-0.5-mRNA-1:cds;Parent=snap_masked-contig1-processed-gene-0.5-mRNA-1
> contig1 snap_masked match 20468 21193 42.956 + . ID=contig1:hit:5240:4.5.0.0;Name=snap_masked-contig1-abinit-gene-0.5-mRNA-1;target_length=4075195
> contig1 snap_masked match_part 20468 21193 42.956 + . ID=contig1:hsp:12911:4.5.0.0;Parent=contig1:hit:5240:4.5.0.0;Target=snap_masked-contig1-abinit-gene-0.5-mRNA-1 1 726 +;Gap=M726
> contig1 est_gff:est2genome expressed_sequence_match 20468 21193 3630 + . ID=contig1:hit:1051:3.12.0.0;Name=jgi|test_1|140804|est;target_length=726;aligned_coverage=100;aligned_identity=100;aligned_coverage=100;aligned_identity=100;score=3630;target_length=726
> contig1 est_gff:est2genome match_part 20468 21193 3630 + . ID=contig1:hsp:1166:3.12.0.0;Parent=contig1:hit:1051:3.12.0.0;Target=jgi|test_1|140804|est 1 726 +;Gap=M726
>
> Please could anyone shed come light on this?
>
>
> Many thanks in advance.
>
> Urmi
>
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