Hak-Min Kim NNO

 

 

Nomura’s jellyfish genome

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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

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

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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

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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

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5. Methods

 

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