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Created page with "<p><span style="font-size:20px"><strong>KOREF</strong></span></p> <p><span style="font-size:16px">1. Raw data and project folder information</span></p> <ol style="list-style-ty..."
<p><span style="font-size:20px"><strong>KOREF</strong></span></p>
<p><span style="font-size:16px">1. Raw data and project folder information</span></p>
<ol style="list-style-type:upper-alpha">
<li><span style="font-size:16px">Project folder:</span>
<ol style="list-style-type:lower-roman">
<li><span style="font-size:16px">KPGP서버 /BiO/Research/Project1/TGI-KOREF-Genome-2013-06/</span></li>
<li><span style="font-size:16px">KOREF서버 /BiO/Research/Project1/TGI-KOREF-Genome-2013-06/</span></li>
</ol>
</li>
<li><span style="font-size:16px">Raw data information: <a href="http://in.tgi.kr/index.php/Overall_Data_Information">http://in.tgi.kr/index.php/Overall_Data_Information</a></span></li>
</ol>
<p style="margin-left:40.0pt"> </p>
<p><span style="font-size:16px">2. Paper status: Published ([[</span><a href="https://www.nature.com/articles/ncomms13637">https://www.nature.com/articles/ncomms13637</a><span style="font-size:16px">|An ethnically relevant consensus Korean reference genome is a step towards personal reference genomes]]. <em>Nature communications</em>, 2016)</span></p>
<p style="margin-left:38.0pt"> </p>
<p><span style="font-size:16px">3. Analysis result</span></p>
<ol style="list-style-type:upper-alpha">
<li><span style="font-size:16px">Assembly result: KPGP서버 /BiO/Research/Project1/TGI-KOREF-Genome-2013-06/Assembly</span></li>
<li><span style="font-size:16px">Annotation result (Gene set / Repeat): KPGP서버 /BiO/Research/Project1/TGI-KOREF-Genome-2013-06/Annotation</span>
<ol style="list-style-type:lower-roman">
<li><span style="font-size:16px">Ethnic gene prediction result: KOREF서버 /BiO/Research/Project1/TGI-KOREF-Genome-2013-06/GenePrediction_for_All_assemblies_BestHit</span></li>
<li><span style="font-size:16px">Ethnic repeat masking result: KPGP서버 /BiO/Research/Project1/TGI-KOREF-Genome-2013-06/Ethnic_RepeatMask</span></li>
</ol>
</li>
<li><span style="font-size:16px">Mitochondria assembly result: KPGP서버 /BiO/Research/Project1/TGI-KOREF-Genome-2013-06/Mitochondria_assembly</span></li>
<li><span style="font-size:16px">Ethnic assemblies segmental duplication result: KPGP서버 /BiO/Research/Project1/TGI-KOREF-Genome-2013-06/SegmentalDuplication</span></li>
</ol>
<p style="margin-left:60.0pt"> </p>
<p><span style="font-size:16px">4. Related script</span></p>
<ol style="list-style-type:upper-alpha">
<li><span style="font-size:16px">Repeat maksing</span>
<ol style="list-style-type:lower-roman">
<li><span style="font-size:16px">Run repeat masking: KPGP서버 /BiO/Research/Project1/TGI-KOREF-Genome-2013-06/Ethnic_RepeatMask/0_RepeatMasking_the_genome.pl</span></li>
<li><span style="font-size:16px">Count the hetero variants in repeat region: KPGP서버 /BiO/Research/Project1/TGI-KOREF-Genome-2013-06/Ethnic_RepeatMask/1_Count_hetero_variants_in_repeat_region_withArray.pl</span></li>
</ol>
</li>
<li><span style="font-size:16px">Sspace_longread (scaffolding program)</span>
<ol style="list-style-type:lower-roman">
<li><span style="font-size:16px">Run Sspace_longread with Pacbio and Moleculo data: KPGP서버 /BiO/Research/Project1/TGI-KOREF-Genome-2013-06/Assembly/3.Pacbio_Moleculo_SSPACE_with_2/script/0_SSPACE-longread_run_with_Pacbio_Moleculo.pl</span></li>
</ol>
</li>
<li><span style="font-size:16px">Exonerate unmapped count script: KOREF서버 /BiO/Research/Project1/TGI-KOREF-Genome-2013-06/GenePrediction_for_All_assemblies_BestHit/Exonerate_unmpped_count.pl</span></li>
</ol>
<p style="margin-left:60.0pt"> </p>
<p><span style="font-size:16px">5. Methods</span></p>
<ol style="list-style-type:upper-alpha">
<li><span style="font-size:16px">All methods are described in the method & material section of the published article.</span></li>
</ol>
<p><span style="font-size:16px">1. Raw data and project folder information</span></p>
<ol style="list-style-type:upper-alpha">
<li><span style="font-size:16px">Project folder:</span>
<ol style="list-style-type:lower-roman">
<li><span style="font-size:16px">KPGP서버 /BiO/Research/Project1/TGI-KOREF-Genome-2013-06/</span></li>
<li><span style="font-size:16px">KOREF서버 /BiO/Research/Project1/TGI-KOREF-Genome-2013-06/</span></li>
</ol>
</li>
<li><span style="font-size:16px">Raw data information: <a href="http://in.tgi.kr/index.php/Overall_Data_Information">http://in.tgi.kr/index.php/Overall_Data_Information</a></span></li>
</ol>
<p style="margin-left:40.0pt"> </p>
<p><span style="font-size:16px">2. Paper status: Published ([[</span><a href="https://www.nature.com/articles/ncomms13637">https://www.nature.com/articles/ncomms13637</a><span style="font-size:16px">|An ethnically relevant consensus Korean reference genome is a step towards personal reference genomes]]. <em>Nature communications</em>, 2016)</span></p>
<p style="margin-left:38.0pt"> </p>
<p><span style="font-size:16px">3. Analysis result</span></p>
<ol style="list-style-type:upper-alpha">
<li><span style="font-size:16px">Assembly result: KPGP서버 /BiO/Research/Project1/TGI-KOREF-Genome-2013-06/Assembly</span></li>
<li><span style="font-size:16px">Annotation result (Gene set / Repeat): KPGP서버 /BiO/Research/Project1/TGI-KOREF-Genome-2013-06/Annotation</span>
<ol style="list-style-type:lower-roman">
<li><span style="font-size:16px">Ethnic gene prediction result: KOREF서버 /BiO/Research/Project1/TGI-KOREF-Genome-2013-06/GenePrediction_for_All_assemblies_BestHit</span></li>
<li><span style="font-size:16px">Ethnic repeat masking result: KPGP서버 /BiO/Research/Project1/TGI-KOREF-Genome-2013-06/Ethnic_RepeatMask</span></li>
</ol>
</li>
<li><span style="font-size:16px">Mitochondria assembly result: KPGP서버 /BiO/Research/Project1/TGI-KOREF-Genome-2013-06/Mitochondria_assembly</span></li>
<li><span style="font-size:16px">Ethnic assemblies segmental duplication result: KPGP서버 /BiO/Research/Project1/TGI-KOREF-Genome-2013-06/SegmentalDuplication</span></li>
</ol>
<p style="margin-left:60.0pt"> </p>
<p><span style="font-size:16px">4. Related script</span></p>
<ol style="list-style-type:upper-alpha">
<li><span style="font-size:16px">Repeat maksing</span>
<ol style="list-style-type:lower-roman">
<li><span style="font-size:16px">Run repeat masking: KPGP서버 /BiO/Research/Project1/TGI-KOREF-Genome-2013-06/Ethnic_RepeatMask/0_RepeatMasking_the_genome.pl</span></li>
<li><span style="font-size:16px">Count the hetero variants in repeat region: KPGP서버 /BiO/Research/Project1/TGI-KOREF-Genome-2013-06/Ethnic_RepeatMask/1_Count_hetero_variants_in_repeat_region_withArray.pl</span></li>
</ol>
</li>
<li><span style="font-size:16px">Sspace_longread (scaffolding program)</span>
<ol style="list-style-type:lower-roman">
<li><span style="font-size:16px">Run Sspace_longread with Pacbio and Moleculo data: KPGP서버 /BiO/Research/Project1/TGI-KOREF-Genome-2013-06/Assembly/3.Pacbio_Moleculo_SSPACE_with_2/script/0_SSPACE-longread_run_with_Pacbio_Moleculo.pl</span></li>
</ol>
</li>
<li><span style="font-size:16px">Exonerate unmapped count script: KOREF서버 /BiO/Research/Project1/TGI-KOREF-Genome-2013-06/GenePrediction_for_All_assemblies_BestHit/Exonerate_unmpped_count.pl</span></li>
</ol>
<p style="margin-left:60.0pt"> </p>
<p><span style="font-size:16px">5. Methods</span></p>
<ol style="list-style-type:upper-alpha">
<li><span style="font-size:16px">All methods are described in the method & material section of the published article.</span></li>
</ol>
