<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="">Run A —> no gene prediction, just cut and paste of transcript/protein alignments to generate rough models.<div class="">Run B —> Gene predictions based on training using only highly conserved subset of genes (you will have low sensitivity)</div><div class=""><div>Run C —> Gene predictions based on training using broader gene set. Higher sensitivity but potentially lower specificity (sensitivity gains should outweigh any specificity loss).</div><div><br class=""></div><div>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 —> <a href="https://wjidea.github.io/defusion/installation.html" class="">https://wjidea.github.io/defusion/installation.html</a></div><div><br class=""></div><div>—Carson</div><div><br class=""></div><div><br class=""></div><div><br class=""><blockquote type="cite" class=""><div class="">On Mar 21, 2018, at 3:05 AM, Urmi <<a href="mailto:urmi208@gmail.com" class="">urmi208@gmail.com</a>> wrote:</div><br class="Apple-interchange-newline"><div class=""><div dir="ltr" class=""><p style="box-sizing:border-box;margin:0px 0px 10px;color:rgb(51,51,51);font-family:sans-serif;font-size:13px;font-style:normal;font-variant-ligatures:normal;font-variant-caps:normal;font-weight:400;letter-spacing:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;background-color:rgb(255,255,255);text-decoration-style:initial;text-decoration-color:initial" class="">Hello maker community,</p><p style="box-sizing:border-box;margin:0px 0px 10px;color:rgb(51,51,51);font-family:sans-serif;font-size:13px;font-style:normal;font-variant-ligatures:normal;font-variant-caps:normal;font-weight:400;letter-spacing:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;background-color:rgb(255,255,255);text-decoration-style:initial;text-decoration-color:initial" class="">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:</p><ol style="box-sizing:border-box;margin-top:0px;margin-bottom:10px;color:rgb(51,51,51);font-family:sans-serif;font-size:13px;font-style:normal;font-variant-ligatures:normal;font-variant-caps:normal;font-weight:400;letter-spacing:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;background-color:rgb(255,255,255);text-decoration-style:initial;text-decoration-color:initial" class=""><li style="box-sizing:border-box" class="">Run maker with repeat masking and providing transcript and protein sequences from related species (Run A)</li><li style="box-sizing:border-box" class="">Create SNAP model with CEGMA</li><li style="box-sizing:border-box" class="">Train Augustus with BUSCO</li><li style="box-sizing:border-box" class="">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)</li><li style="box-sizing:border-box" class="">Create SNAP model from run B.</li><li style="box-sizing:border-box" class="">Train Augustus with transcripts from run B and BUSCO</li><li style="box-sizing:border-box" class="">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</li></ol><p style="box-sizing:border-box;margin:0px 0px 10px;color:rgb(51,51,51);font-family:sans-serif;font-size:13px;font-style:normal;font-variant-ligatures:normal;font-variant-caps:normal;font-weight:400;letter-spacing:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;background-color:rgb(255,255,255);text-decoration-style:initial;text-decoration-color:initial" class="">As a result of this, I get following gene numbers:</p><ul style="box-sizing:border-box;margin-top:0px;margin-bottom:10px;color:rgb(51,51,51);font-family:sans-serif;font-size:13px;font-style:normal;font-variant-ligatures:normal;font-variant-caps:normal;font-weight:400;letter-spacing:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;background-color:rgb(255,255,255);text-decoration-style:initial;text-decoration-color:initial" class=""><li style="box-sizing:border-box" class="">run A: 12796 total genes out of which 12771 have AED < 0.5</li><li style="box-sizing:border-box" class="">run B:10713 total genes out of which 10701 have AED < 0.5</li><li style="box-sizing:border-box" class="">run C: 12651 total genes out of which 12582 have AED < 0.5</li></ul><span style="color:rgb(51,51,51);font-family:sans-serif;font-size:13px" class="">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. <span style="color:rgb(51,51,51);font-family:sans-serif;font-size:13px;font-style:normal;font-variant-ligatures:normal;font-variant-caps:normal;font-weight:400;letter-spacing:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;background-color:rgb(255,255,255);text-decoration-style:initial;text-decoration-color:initial;float:none;display:inline" class="">I don't understand why there is gene loss for run B.<span class=""> Here is an example:</span></span></span><div class=""><font color="#333333" face="sans-serif" class=""><br class=""></font></div><div class=""><font color="#333333" face="sans-serif" class=""><b class="">RunA</b><br class=""></font><div class=""><font color="#333333" face="sans-serif" class=""><br class=""></font></div><div class=""><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex"><font color="#333333" face="sans-serif" class=""><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex">contig1 maker gene 20468 21193 . + . ID=maker-contig1-exonerate_protein2genome-gene-0.34;Name=maker-contig1-exonerate_protein2genome-gene-0.34</blockquote><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex">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</blockquote><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex">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</blockquote><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex">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</blockquote><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex">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</blockquote><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex">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</blockquote><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex">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</blockquote><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex">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</blockquote></font></blockquote><div class=""><div class=""><font color="#333333" face="sans-serif" class=""><br class=""></font></div><div class=""><font color="#333333" face="sans-serif" class=""><b class="">RunB:</b></font></div><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex"><font color="#333333" face="sans-serif" class=""><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex">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</blockquote><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex">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</blockquote></font></blockquote><div class=""><br class=""></div><div class=""><b class="">RunC: </b></div><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex"><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex">contig1 maker gene 20468 21193 . + . ID=snap_masked-contig1-processed-gene-0.5;Name=snap_masked-contig1-processed-gene-0.5</blockquote><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex">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</blockquote><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex">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</blockquote><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex">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</blockquote><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex">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</blockquote><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex">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</blockquote><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex">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</blockquote><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex">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</blockquote></blockquote><div class=""><font color="#333333" face="sans-serif" class=""><br class=""></font></div><div class=""><span style="color:rgb(51,51,51);font-family:sans-serif;font-size:13px" class="">Please could anyone shed come light on this?</span><br class=""></div><p style="box-sizing:border-box;margin:0px 0px 10px;color:rgb(51,51,51);font-family:sans-serif;font-size:13px;font-style:normal;font-variant-ligatures:normal;font-variant-caps:normal;font-weight:400;letter-spacing:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;background-color:rgb(255,255,255);text-decoration-style:initial;text-decoration-color:initial" class=""><br class=""></p><p style="box-sizing:border-box;margin:0px 0px 10px;color:rgb(51,51,51);font-family:sans-serif;font-size:13px;font-style:normal;font-variant-ligatures:normal;font-variant-caps:normal;font-weight:400;letter-spacing:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;background-color:rgb(255,255,255);text-decoration-style:initial;text-decoration-color:initial" class="">Many thanks in advance.</p><p style="box-sizing:border-box;margin:0px 0px 10px;color:rgb(51,51,51);font-family:sans-serif;font-size:13px;font-style:normal;font-variant-ligatures:normal;font-variant-caps:normal;font-weight:400;letter-spacing:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;background-color:rgb(255,255,255);text-decoration-style:initial;text-decoration-color:initial" class="">Urmi</p></div></div></div></div>
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