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Carson,<br>
<br>
Analyzing the output of a MAKER run on a rice-sized genome I noticed
that some gene models (~10%) overlap with TE coding regions. As a QC
step, I used BEDtools to determine the intersection of "CDS" and
"repeatmasker" or "repeatrunner" and some 2400 genes overlap for at
least 30% of their respective length. I am wondering how the gene
models still appear in the final output, since I thought that the
masking step was giving us the absoulte confirmation that in our
endogenous gene list we do not include TE coding regions. Here below
an example of a gene (attached picture too):<br>
<br>
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<colgroup span="5" width="85"></colgroup> <colgroup width="35"></colgroup>
<colgroup span="2" width="31"></colgroup> <colgroup width="85"></colgroup>
<tbody>
<tr>
<td align="LEFT" height="16">ObracChr10</td>
<td align="LEFT">maker</td>
<td align="LEFT">mRNA</td>
<td sdval="355056" sdnum="1033;0;#,##0" align="RIGHT">355,056</td>
<td sdval="358075" sdnum="1033;0;#,##0" align="RIGHT">358,075</td>
<td align="LEFT">.</td>
<td align="LEFT">-</td>
<td align="LEFT">.</td>
<td align="LEFT">ID=Obrac10g00240.1;Parent=Obrac10g00240;Name=Obrac10g00240.1;_AED=0.24;_eAED=0.24;_QI=0|0.66|0.5|1|1|1|4|0|788</td>
</tr>
<tr>
<td align="LEFT" height="16">ObracChr10</td>
<td align="LEFT">maker</td>
<td align="LEFT">exon</td>
<td sdval="355056" sdnum="1033;0;#,##0" align="RIGHT">355,056</td>
<td sdval="356874" sdnum="1033;0;#,##0" align="RIGHT">356,874</td>
<td align="LEFT">.</td>
<td align="LEFT">-</td>
<td align="LEFT">.</td>
<td align="LEFT">ID=Obrac10g00240.1:exon:4;Parent=Obrac10g00240.1</td>
</tr>
<tr>
<td align="LEFT" height="16">ObracChr10</td>
<td align="LEFT">maker</td>
<td align="LEFT">exon</td>
<td sdval="356965" sdnum="1033;0;#,##0" align="RIGHT">356,965</td>
<td sdval="357081" sdnum="1033;0;#,##0" align="RIGHT">357,081</td>
<td align="LEFT">.</td>
<td align="LEFT">-</td>
<td align="LEFT">.</td>
<td align="LEFT">ID=Obrac10g00240.1:exon:3;Parent=Obrac10g00240.1</td>
</tr>
<tr>
<td align="LEFT" height="16">ObracChr10</td>
<td align="LEFT">maker</td>
<td align="LEFT">exon</td>
<td sdval="357209" sdnum="1033;0;#,##0" align="RIGHT">357,209</td>
<td sdval="357319" sdnum="1033;0;#,##0" align="RIGHT">357,319</td>
<td align="LEFT">.</td>
<td align="LEFT">-</td>
<td align="LEFT">.</td>
<td align="LEFT">ID=Obrac10g00240.1:exon:2;Parent=Obrac10g00240.1</td>
</tr>
<tr>
<td align="LEFT" height="16">ObracChr10</td>
<td align="LEFT">maker</td>
<td align="LEFT">exon</td>
<td sdval="357756" sdnum="1033;0;#,##0" align="RIGHT">357,756</td>
<td sdval="358075" sdnum="1033;0;#,##0" align="RIGHT">358,075</td>
<td align="LEFT">.</td>
<td align="LEFT">-</td>
<td align="LEFT">.</td>
<td align="LEFT">ID=Obrac10g00240.1:exon:1;Parent=Obrac10g00240.1</td>
</tr>
<tr>
<td align="LEFT" height="16">ObracChr10</td>
<td align="LEFT">maker</td>
<td align="LEFT">CDS</td>
<td sdval="357756" sdnum="1033;0;#,##0" align="RIGHT">357,756</td>
<td sdval="358075" sdnum="1033;0;#,##0" align="RIGHT">358,075</td>
<td align="LEFT">.</td>
<td align="LEFT">-</td>
<td sdval="2" sdnum="1033;" align="RIGHT">2</td>
<td align="LEFT">ID=Obrac10g00240.1:cds;Parent=Obrac10g00240.1</td>
</tr>
<tr>
<td align="LEFT" height="16">ObracChr10</td>
<td align="LEFT">maker</td>
<td align="LEFT">CDS</td>
<td sdval="357209" sdnum="1033;0;#,##0" align="RIGHT">357,209</td>
<td sdval="357319" sdnum="1033;0;#,##0" align="RIGHT">357,319</td>
<td align="LEFT">.</td>
<td align="LEFT">-</td>
<td sdval="2" sdnum="1033;" align="RIGHT">2</td>
<td align="LEFT">ID=Obrac10g00240.1:cds;Parent=Obrac10g00240.1</td>
</tr>
<tr>
<td align="LEFT" height="16">ObracChr10</td>
<td align="LEFT">maker</td>
<td align="LEFT">CDS</td>
<td sdval="356965" sdnum="1033;0;#,##0" align="RIGHT">356,965</td>
<td sdval="357081" sdnum="1033;0;#,##0" align="RIGHT">357,081</td>
<td align="LEFT">.</td>
<td align="LEFT">-</td>
<td sdval="2" sdnum="1033;" align="RIGHT">2</td>
<td align="LEFT">ID=Obrac10g00240.1:cds;Parent=Obrac10g00240.1</td>
</tr>
<tr>
<td align="LEFT" height="16">ObracChr10</td>
<td align="LEFT">maker</td>
<td align="LEFT">CDS</td>
<td sdval="355056" sdnum="1033;0;#,##0" align="RIGHT">355,056</td>
<td sdval="356874" sdnum="1033;0;#,##0" align="RIGHT">356,874</td>
<td align="LEFT">.</td>
<td align="LEFT">-</td>
<td sdval="0" sdnum="1033;" align="RIGHT">0</td>
<td align="LEFT">ID=Obrac10g00240.1:cds;Parent=Obrac10g00240.1</td>
</tr>
<tr>
<td align="LEFT" height="16"><br>
</td>
<td align="LEFT"><br>
</td>
<td align="LEFT"><br>
</td>
<td sdnum="1033;0;#,##0" align="LEFT"><br>
</td>
<td sdnum="1033;0;#,##0" align="LEFT"><br>
</td>
<td align="LEFT"><br>
</td>
<td align="LEFT"><br>
</td>
<td align="LEFT"><br>
</td>
<td align="LEFT"><br>
</td>
</tr>
<tr>
<td align="LEFT" height="16"><br>
</td>
<td align="LEFT"><br>
</td>
<td align="LEFT"><br>
</td>
<td sdnum="1033;0;#,##0" align="LEFT"><br>
</td>
<td sdnum="1033;0;#,##0" align="LEFT"><br>
</td>
<td align="LEFT"><br>
</td>
<td align="LEFT"><br>
</td>
<td align="LEFT"><br>
</td>
<td align="LEFT"><br>
</td>
</tr>
<tr>
<td align="LEFT" height="17">ObracChr10</td>
<td align="LEFT">repeatrunner</td>
<td align="LEFT">match_part</td>
<td sdval="357755" sdnum="1033;0;#,##0" align="RIGHT">357,755</td>
<td sdval="358084" sdnum="1033;0;#,##0" align="RIGHT">358,084</td>
<td sdval="566" sdnum="1033;" align="RIGHT">566</td>
<td align="LEFT">-</td>
<td align="LEFT">.</td>
<td align="LEFT">ID=ObracChr10:hsp:75:1.3.0.3;Parent=ObracChr10:hit:75:1.3.0.3;Target=DTM_gi_125573769_gb_EAZ15053.1hypothetical
117 226 +320</td>
</tr>
<tr>
<td align="LEFT" height="17">ObracChr10</td>
<td align="LEFT">repeatrunner</td>
<td align="LEFT">protein_match</td>
<td sdval="357755" sdnum="1033;0;#,##0" align="RIGHT">357,755</td>
<td sdval="358084" sdnum="1033;0;#,##0" align="RIGHT">358,084</td>
<td sdval="566" sdnum="1033;" align="RIGHT">566</td>
<td align="LEFT">-</td>
<td align="LEFT">.</td>
<td align="LEFT">ID=ObracChr10:hit:75:1.3.0.3;Name=DTM_gi_125573769_gb_EAZ15053.1hypothetical;Target=DTM_gi_125573769_gb_EAZ15053.1hypothetical
117 226 +320</td>
</tr>
<tr>
<td align="LEFT" height="17">ObracChr10</td>
<td align="LEFT">repeatrunner</td>
<td align="LEFT">match_part</td>
<td sdval="357202" sdnum="1033;0;#,##0" align="RIGHT">357,202</td>
<td sdval="357294" sdnum="1033;0;#,##0" align="RIGHT">357,294</td>
<td sdval="142" sdnum="1033;" align="RIGHT">142</td>
<td align="LEFT">-</td>
<td align="LEFT">.</td>
<td align="LEFT">ID=ObracChr10:hsp:74:1.3.0.3;Parent=ObracChr10:hit:74:1.3.0.3;Target=DTM_gi_125573769_gb_EAZ15053.1hypothetical
264 294 +86</td>
</tr>
<tr>
<td align="LEFT" height="17">ObracChr10</td>
<td align="LEFT">repeatrunner</td>
<td align="LEFT">protein_match</td>
<td sdval="357202" sdnum="1033;0;#,##0" align="RIGHT">357,202</td>
<td sdval="357294" sdnum="1033;0;#,##0" align="RIGHT">357,294</td>
<td sdval="142" sdnum="1033;" align="RIGHT">142</td>
<td align="LEFT">-</td>
<td align="LEFT">.</td>
<td align="LEFT">ID=ObracChr10:hit:74:1.3.0.3;Name=DTM_gi_125573769_gb_EAZ15053.1hypothetical;Target=DTM_gi_125573769_gb_EAZ15053.1hypothetical
264 294 +86</td>
</tr>
<tr>
<td align="LEFT" height="17">ObracChr10</td>
<td align="LEFT">repeatrunner</td>
<td align="LEFT">match_part</td>
<td sdval="355059" sdnum="1033;0;#,##0" align="RIGHT">355,059</td>
<td sdval="357092" sdnum="1033;0;#,##0" align="RIGHT">357,092</td>
<td sdval="3367" sdnum="1033;" align="RIGHT">3367</td>
<td align="LEFT">-</td>
<td align="LEFT">.</td>
<td align="LEFT">ID=ObracChr10:hsp:73:1.3.0.3;Parent=ObracChr10:hit:73:1.3.0.3;Target=DTM_gi_125573769_gb_EAZ15053.1hypothetical
289 937 +1816</td>
</tr>
<tr>
<td align="LEFT" height="17">ObracChr10</td>
<td align="LEFT">repeatrunner</td>
<td align="LEFT">protein_match</td>
<td sdval="355059" sdnum="1033;0;#,##0" align="RIGHT">355,059</td>
<td sdval="357092" sdnum="1033;0;#,##0" align="RIGHT">357,092</td>
<td sdval="3367" sdnum="1033;" align="RIGHT">3367</td>
<td align="LEFT">-</td>
<td align="LEFT">.</td>
<td align="LEFT">ID=ObracChr10:hit:73:1.3.0.3;Name=DTM_gi_125573769_gb_EAZ15053.1hypothetical;Target=DTM_gi_125573769_gb_EAZ15053.1hypothetical
289 937 +1816</td>
</tr>
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<br>
This result is valid both for output lines from repeatmasker or
repeatrunner, and the gene models come from either FGENESH or SNAP
predictions.<br>
How can I explain this problem?<br>
Thanks,<br>
<br>
Dario<br>
<br>
<br>
<br>
<br>
<pre class="moz-signature" cols="72">--
Dario Copetti, PhD
Research Associate
Arizona Genomics Institute
University of Arizona - BIO5
1657 E. Helen St.
Tucson, AZ 85721
<a class="moz-txt-link-abbreviated" href="http://www.genome.arizona.edu">www.genome.arizona.edu</a>
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