Difference between revisions of "Hak-Min Kim Leopard"

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<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><span style="font-size:16px"><strong>2. Paper status</strong>: Published (<a href="https://genomebiology.biomedcentral.com/articles/10.1186/s13059-016-1071-4">Comparison of carnivore, omnivore, and herbivore mammalian genomes with a new leopard assembly.</a> <em>Genome biology</em>, 2016)</span></p>
  
 
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<ol style="list-style-type:upper-alpha">
 
<ol style="list-style-type:upper-alpha">
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<li><span style="font-size:16px">Assembly refinement with Moleculo (Gap filling with moleculo)</span></li>
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<li><span style="font-size:16px">Assembly refinement with Moleculo (Gap filling with moleculo) ==&gt; It is composed of 6 scripts and plays the role of gap filling using Moleculo. Execute script 0 to 5 sequentially</span>
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</ol>
 
  
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<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>
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<ol style="list-style-type:lower-roman">
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<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>
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<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>
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<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>
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<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>
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<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>
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<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>
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<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>
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<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>
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<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>
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<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>
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<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>
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</ol>
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<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>
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</li>
 
<li><span style="font-size:16px">Calculation Moleculo length and yield distribution</span>
 
<li><span style="font-size:16px">Calculation Moleculo length and yield distribution</span>
 
<ol style="list-style-type:lower-roman">
 
<ol style="list-style-type:lower-roman">

Latest revision as of 16:01, 20 August 2019

 

 

Leopard genome

 

1. Raw data and project folder information

  1. Project folder
    1. Whale서버 /BiO/Research/Project1/TGI-AmurLeopard-Genome-2015-03
  2. Raw data information:
    1. Illumina short/mate reads: Whale서버 /BiO/Research/Project1/TGI-AmurLeopard-Genome-2015-03/0.Rawdata
    2. Moleculo long reads: Whale서버 /BiO/Research/Project1/TGI-AmurLeopard-Genome-2015-03/0.Rawdata/Moleculo

 

2. Paper status: Published (Comparison of carnivore, omnivore, and herbivore mammalian genomes with a new leopard assembly. Genome biology, 2016)

 

3. Analysis result

  1. Assembly result: /BiO/Research/Project1/TGI-AmurLeopard-Genome-2015-03/13.SNV_INDEL_substitution_scaffold/Amurleopard.K63.Gapclosed_SNV.INDEL.substituted.new.fa
  2. Annotation result:
    1. Gene set (Paper version): /BiO/Research/Project1/TGI-AmurLeopard-Genome-2015-03/24.FinalGenes/Leopard
    2. Gene set (NCBI version):
      1. GFF: 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
      2. Protein seq: 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
      3. CDS seq: 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
  3. Orthologous gene cluster & gene expansion and contraction: /BiO/Research/Project1/TGI-AmurLeopard-Genome-2015-03/25.Orthologous_gene_cluster_Input/OthoMCL_result_Tasmanian
  4. Felidae species mapping result: /BiO/Research/Project1/TGI-AmurLeopard-Genome-2015-03/23.Multi-mapping-Felidae-species
  5. Selective sweep (Highly conserved region): KOREF서버 /BiO/Research/Project1/TGI-AmurLeopard-Genome-2015-03/Seletive_sweep/Selective_sweep/Result_FamilyLevel
  6. Pairwise sequentially Markovian coalescent analysis (PSMC): /BiO/Research/Project1/TGI-AmurLeopard-Genome-2015-03/Workspace/tgikimhh/PSMC

 

4. Related script

  1. Assembly refinement with Moleculo (Gap filling with moleculo) ==> It is composed of 6 scripts and plays the role of gap filling using Moleculo. Execute script 0 to 5 sequentially
    1. /BiO/Research/Project1/TGI-AmurLeopard-Genome-2015-03/15.Moleculo_Align_with_substituted_scaffold_BWA/0_mapping_moleculo_to_Amurleopard.pl*
    2. /BiO/Research/Project1/TGI-AmurLeopard-Genome-2015-03/15.Moleculo_Align_with_substituted_scaffold_BWA/1_Covered_N_base_detect.pl*
    3. /BiO/Research/Project1/TGI-AmurLeopard-Genome-2015-03/15.Moleculo_Align_with_substituted_scaffold_BWA/2_Extract_moleculo_reads_from_N_region.pl*
    4. /BiO/Research/Project1/TGI-AmurLeopard-Genome-2015-03/15.Moleculo_Align_with_substituted_scaffold_BWA/3_Replace_scaffold_with_moleculo.pl*
    5. /BiO/Research/Project1/TGI-AmurLeopard-Genome-2015-03/15.Moleculo_Align_with_substituted_scaffold_BWA/4_Substituted_N_count.pl*
    6. /BiO/Research/Project1/TGI-AmurLeopard-Genome-2015-03/15.Moleculo_Align_with_substituted_scaffold_BWA/5_Scaffold_finalize.pl*
  2. Calculation Moleculo length and yield distribution
    1. /BiO/Research/Project1/TGI-AmurLeopard-Genome-2015-03/0.Rawdata/Moleculo/0_length_distribution_and_yield_distribution.pl

 

5. Methods

  1. All methods are described in the method & material section of the published article.

 

 

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