Difference between revisions of "Hak-Min Kim KOREF"

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<li>Assembly process<br />
 
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<li><span style="font-size:16px">All methods are described in the method &amp; material section of the published article.</span></li>
 
<li><span style="font-size:16px">All methods are described in the method &amp; material section of the published article.</span></li>
 
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Latest revision as of 12:08, 21 August 2019

 

 

KOREF

 

1. Raw data and project folder information

  1. Project folder:
    1. KPGP서버 /BiO/Research/Project1/TGI-KOREF-Genome-2013-06/
    2. KOREF서버 /BiO/Research/Project1/TGI-KOREF-Genome-2013-06/
  2. Raw data information: http://in.tgi.kr/index.php/Overall_Data_Information

 

2. Paper status: Published (An ethnically relevant consensus Korean reference genome is a step towards personal reference genomes. Nature communications, 2016)

 

3. Analysis result

  1. Assembly result: KPGP서버 /BiO/Research/Project1/TGI-KOREF-Genome-2013-06/Assembly
  2. Annotation result (Gene set / Repeat): KPGP서버 /BiO/Research/Project1/TGI-KOREF-Genome-2013-06/Annotation
    1. Ethnic gene prediction result: KOREF서버 /BiO/Research/Project1/TGI-KOREF-Genome-2013-06/GenePrediction_for_All_assemblies_BestHit
    2. Ethnic repeat masking result: KPGP서버 /BiO/Research/Project1/TGI-KOREF-Genome-2013-06/Ethnic_RepeatMask
  3. Mitochondria assembly result: KPGP서버 /BiO/Research/Project1/TGI-KOREF-Genome-2013-06/Mitochondria_assembly
  4. Ethnic assemblies segmental duplication result: KPGP서버 /BiO/Research/Project1/TGI-KOREF-Genome-2013-06/SegmentalDuplication

 

4. Related script

  1. Repeat maksing
    1. Run repeat masking: KPGP서버 /BiO/Research/Project1/TGI-KOREF-Genome-2013-06/Ethnic_RepeatMask/0_RepeatMasking_the_genome.pl
    2. 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
  2. Sspace_longread (scaffolding program)
    1. 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
  3. Exonerate unmapped count script: KOREF서버 /BiO/Research/Project1/TGI-KOREF-Genome-2013-06/GenePrediction_for_All_assemblies_BestHit/Exonerate_unmpped_count.pl

 

5. Methods

  1. Assembly process


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