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Hak-Min Kim Leopard

5,741 bytes added, 15:56, 20 August 2019
Created page with "<p><span style="font-size:20px"><strong>Leopard genome</strong></span></p> <hr /> <p> </p> <p><strong><span style="font-size:16px">1. Raw data and project folder informati..."
<p><span style="font-size:20px"><strong>Leopard genome</strong></span></p>

<hr />
<p>&nbsp;</p>

<p><strong><span style="font-size:16px">1. Raw data and project folder information</span></strong></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">Whale서버 /BiO/Research/Project1/TGI-AmurLeopard-Genome-2015-03</span></li>
</ol>
</li>
<li><span style="font-size:16px">Raw data information:</span>
<ol style="list-style-type:lower-roman">
<li><span style="font-size:16px">Illumina short/mate reads: Whale서버 /BiO/Research/Project1/TGI-AmurLeopard-Genome-2015-03/0.Rawdata</span></li>
<li><span style="font-size:16px">Moleculo long reads: Whale서버 /BiO/Research/Project1/TGI-AmurLeopard-Genome-2015-03/0.Rawdata/Moleculo</span></li>
</ol>
</li>
</ol>

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<p>&nbsp;</p>

<p><span style="font-size:16px"><strong>2. Paper status</strong>: Published (Comparison of carnivore, omnivore, and herbivore mammalian genomes with a new leopard assembly. <em>Genome biology</em>, 2016)</span></p>

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<p>&nbsp;</p>

<p><strong><span style="font-size:16px">3. Analysis result</span></strong></p>

<ol style="list-style-type:upper-alpha">
<li><span style="font-size:16px">Assembly result: /BiO/Research/Project1/TGI-AmurLeopard-Genome-2015-03/13.SNV_INDEL_substitution_scaffold/Amurleopard.K63.Gapclosed_SNV.INDEL.substituted.new.fa</span></li>
<li><span style="font-size:16px">Annotation result:</span>
<ol style="list-style-type:lower-roman">
<li><span style="font-size:16px">Gene set (Paper version): /BiO/Research/Project1/TGI-AmurLeopard-Genome-2015-03/24.FinalGenes/Leopard</span></li>
<li><span style="font-size:16px">Gene set (NCBI version):</span>
<ol>
<li><span style="font-size:16px">GFF: <a href="ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/001/857/705/GCF_001857705.1_PanPar1.0/GCF_001857705.1_PanPar1.0_genomic.gff.gz">ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/001/857/705/GCF_001857705.1_PanPar1.0/GCF_001857705.1_PanPar1.0_genomic.gff.gz</a></span></li>
<li><span style="font-size:16px">Protein seq: <a href="ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/001/857/705/GCF_001857705.1_PanPar1.0/GCF_001857705.1_PanPar1.0_protein.faa.gz">ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/001/857/705/GCF_001857705.1_PanPar1.0/GCF_001857705.1_PanPar1.0_protein.faa.gz</a></span></li>
<li><span style="font-size:16px">CDS seq: <a href="ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/001/857/705/GCF_001857705.1_PanPar1.0/GCF_001857705.1_PanPar1.0_translated_cds.faa.gz">ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/001/857/705/GCF_001857705.1_PanPar1.0/GCF_001857705.1_PanPar1.0_translated_cds.faa.gz</a></span></li>
</ol>
</li>
</ol>
</li>
<li><span style="font-size:16px">Orthologous gene cluster &amp; gene expansion and contraction: /BiO/Research/Project1/TGI-AmurLeopard-Genome-2015-03/25.Orthologous_gene_cluster_Input/OthoMCL_result_Tasmanian</span></li>
<li><span style="font-size:16px">Felidae species mapping result: /BiO/Research/Project1/TGI-AmurLeopard-Genome-2015-03/23.Multi-mapping-Felidae-species</span></li>
<li><span style="font-size:16px">Selective sweep (Highly conserved region): KOREF서버 /BiO/Research/Project1/TGI-AmurLeopard-Genome-2015-03/Seletive_sweep/Selective_sweep/Result_FamilyLevel</span></li>
<li><span style="font-size:16px">Pairwise sequentially Markovian coalescent analysis (PSMC): /BiO/Research/Project1/TGI-AmurLeopard-Genome-2015-03/Workspace/tgikimhh/PSMC</span></li>
</ol>

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<p>&nbsp;</p>

<p><strong><span style="font-size:16px">4. Related script</span></strong></p>

<ol style="list-style-type:upper-alpha">
<li><span style="font-size:16px">Assembly refinement with Moleculo (Gap filling with moleculo)</span></li>
</ol>

<p style="margin-left:40.0pt"><span style="font-size:16px">It is composed of 6 scripts and plays the role of gap filling using Moleculo. Execute script 0 to 5 sequentially</span></p>

<ol>
<li><span style="font-size:16px">/BiO/Research/Project1/TGI-AmurLeopard-Genome-2015-03/15.Moleculo_Align_with_substituted_scaffold_BWA/0_mapping_moleculo_to_Amurleopard.pl*</span></li>
<li><span style="font-size:16px">/BiO/Research/Project1/TGI-AmurLeopard-Genome-2015-03/15.Moleculo_Align_with_substituted_scaffold_BWA/1_Covered_N_base_detect.pl*</span></li>
<li><span style="font-size:16px">/BiO/Research/Project1/TGI-AmurLeopard-Genome-2015-03/15.Moleculo_Align_with_substituted_scaffold_BWA/2_Extract_moleculo_reads_from_N_region.pl*</span></li>
<li><span style="font-size:16px">/BiO/Research/Project1/TGI-AmurLeopard-Genome-2015-03/15.Moleculo_Align_with_substituted_scaffold_BWA/3_Replace_scaffold_with_moleculo.pl*</span></li>
<li><span style="font-size:16px">/BiO/Research/Project1/TGI-AmurLeopard-Genome-2015-03/15.Moleculo_Align_with_substituted_scaffold_BWA/4_Substituted_N_count.pl*</span></li>
<li><span style="font-size:16px">/BiO/Research/Project1/TGI-AmurLeopard-Genome-2015-03/15.Moleculo_Align_with_substituted_scaffold_BWA/5_Scaffold_finalize.pl*</span></li>
<li><span style="font-size:16px">Calculation Moleculo length and yield distribution</span>
<ol style="list-style-type:lower-roman">
<li><span style="font-size:16px">/BiO/Research/Project1/TGI-AmurLeopard-Genome-2015-03/0.Rawdata/Moleculo/0_length_distribution_and_yield_distribution.pl</span></li>
</ol>
</li>
</ol>

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<p>&nbsp;</p>

<p><strong><span style="font-size:16px">5. Methods</span></strong></p>

<ol style="list-style-type:upper-alpha">
<li><span style="font-size:16px">All methods are described in the method &amp; material section of the published article.</span></li>
</ol>

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