Difference between revisions of "Hak-Min Kim NNO"

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<p><strong><span style="font-size:16px">4. Related script</span></strong></p>
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<li><span style="font-size:16px">Retinoic acid response elements (RAREs) analysis pipeline.</span><br />
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<span style="font-size:16px">It is composed of 6 scripts and plays the role of finding RAREs in genome sequence. Execute script 0 to 5 sequentially​</span>
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<p><strong><span style="font-size:16px">5. Methods</span></strong></p>
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Revision as of 12:01, 21 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. Related script

  1. Retinoic acid response elements (RAREs) analysis pipeline.
    It is composed of 6 scripts and plays the role of finding RAREs in genome sequence. Execute script 0 to 5 sequentially​
    1. /BiO/Share/Kit/Pipeline/Hakmin.Kim/Evolution_Analysis/RetinoicAcidResponseElement/0_RAREs_motif_finder.pl
    2. /BiO/Share/Kit/Pipeline/Hakmin.Kim/Evolution_Analysis/RetinoicAcidResponseElement/1_RAREs_nearby_gene_within_targetRange.pl
    3. /BiO/Share/Kit/Pipeline/Hakmin.Kim/Evolution_Analysis/RetinoicAcidResponseElement/2_RAREs_nearby_gene_symbol_within_targetRange.pl
    4. /BiO/Share/Kit/Pipeline/Hakmin.Kim/Evolution_Analysis/RetinoicAcidResponseElement/3_Table3_gene_confirm_with_targetRange.pl
    5. /BiO/Share/Kit/Pipeline/Hakmin.Kim/Evolution_Analysis/RetinoicAcidResponseElement/4_Avg.numberWithin10Kgene.pl
    6. /BiO/Share/Kit/Pipeline/Hakmin.Kim/Evolution_Analysis/RetinoicAcidResponseElement/5_NNO_RAREs_distribution_for_figure.pl

 

5. Methods

 

  1. Assembly process

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

 

 

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