Difference between revisions of "Hak-Min Kim NNO"

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<li>Assembly process<br />
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<img alt="" src="/ckfinder/userfiles/images/4_NNO_assembly_process.PNG" style="height:570px; width:962px" /></li>
 
<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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Revision as of 16:19, 20 August 2019

 

 

Nomura’s jellyfish genome

 

1. Raw data and project folder information

  1. Project folder: Tiger서버 /BiO/Research/Project1/TGI-Jellyfish-Genome-2015-04/
  2. Raw data information:
    1. Pacbio reads: /BiO/Research/Project1/TGI-Jellyfish-Genome-2015-04/0.Rawdata/Falcon_input
    2. Short & Mate pair reads:
      1. /BiO/Research/Project1/TGI-Jellyfish-Genome-2015-04/0.Rawdata/ShortReads
      2. /BiO/Research/Project1/TGI-Jellyfish-Genome-2015-04/0.Rawdata/MatePair
    3. Moleculo: /BiO/Research/Project1/TGI-Jellyfish-Genome-2015-04/0.Rawdata/TSLR
    4. RNA 2 tissue: /BiO/Research/Project1/TGI-Jellyfish-Genome-2015-04/0.Rawdata/RNA

 

2. Paper status: Published (The genome of the giant Nomura's jellyfish sheds light on the early evolution of active predation. BMC biology, 2019)

 

3. Analysis result

  1. Assembly result: /BiO/Research/Project1/TGI-Jellyfish-Genome-2015-04/Final_assembly
  2. Annotation result
    1. Gene set: /BiO/Research/Project1/TGI-Jellyfish-Genome-2015-04/Final_GeneSet
    2. Repeat result: /BiO/Research/Project1/TGI-Jellyfish-Genome-2015-04/10.RepeatAnnotation_9K/Repeat_9K/Report/all.gff
    3. Domain annotation: /BiO/Research/Project1/TGI-Jellyfish-Genome-2015-04/Domain_ExpansionContraction/Domain/NemNom.pep.interproscan.tsv
  3. Orthologous gene cluster & gene family expansion and contraction: /BiO/Research/Project1/TGI-Jellyfish-Genome-2015-04/GeneFamily_ExpansionContraction_final_20170124
  4. Hox genes: /BiO/Research/Project1/TGI-Jellyfish-Genome-2015-04/Specific_topic_gene_examine/HoxGene_new/Final
  5. Wnt genes: /BiO/Research/Project1/TGI-Jellyfish-Genome-2015-04/Specific_topic_gene_examine/Wnt_family
  6. Retinoid acid receptor: /BiO/Research/Project1/TGI-Jellyfish-Genome-2015-04/Specific_topic_gene_examine/Retinoid_X_receptor
  7. Venom candidate: /BiO/Research/Project1/TGI-Jellyfish-Genome-2015-04/Venom_with_hmmer_AurAur

 

4. Methods

  1. Assembly process

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

 

 

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