Difference between revisions of "2017 Taeyoung Lab note"

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== 2017 1.2 ==
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[[2017 Jan Taeyoung Lab note]]
=== Ongoing ===
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==== Jatropha transcriptome Trinity assemble ====
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raw data : 244:/NGS/NGS/JatrophaCurcas/RNA
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Jatropha species transcriptome assemble : Jct,Jcu, Jin, Jgo, Jci, Jpo, Jmu, Jma, Jac, Rco (listed in 244:/NGS/NGS/JatrophaCurcas/RNA/list). All done
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Jatropha organ transcriptome assemble : Leaf, Root, Stem, Female flower, Male flower, LG, SG, Y, B. All done
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==== Cdhit ====
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[[2017 Feb Taeyoung Lab note]]
193:/data2/alima90/program/cdhit/cd-hit -i Y.cds.fa -M 10000 -o Y.cds.fa.cdhit -T 5
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193:/data2/alima90/program/cdhit/cd-hit -i LG.cds.fa -M 10000 -o LG.cds.fa.cdhit -T 5
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==== UV GBS mapping (w/ joinmap) ====
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[[2017 Mar Taeyoung Lab note]]
  
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[[2017 May Taeyoung Lab note]]
  
==== KaKs calculation using scripts provided by MCscanX ====
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[[2017 Sep Taeyoung Lab note]]
  
'''KaKs calculation between Jatropha species'''
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[[2017 Oct Taeyoung Lab note]]
244 :python /alima9002/63_backup/Jatropha/CDS/run.kaks.py
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==== Large Insertion Prediction ====
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[[2017 Nov Taeyoung Lab note]]
===== LIP short primer preparation =====
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'''Primer info'''
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[[2017 Dec Taeyoung Lab note]]
>LIP01short_F
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AACTGAACACAGACAATGAA
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>LIP01short_R
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CAATTTATACACCACCTTAC
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>LIP02short_F
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CTCTTTGTATTTGGTGACAA
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>LIP02short_R
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GTATTAGCAGCTTTTGCTTA
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>LIP03short_F
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AATTGTAAGACATATCCCTC
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>LIP03short_R
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CTGCCCCACTAATAATTAAT
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>LIP04short_F
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TAAAAACAGAACTTGTCCAC
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>LIP04short_R
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ATCACAAGACTGAACAAGTA
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>LIP05short_F
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ATTGACATAAGGTTGCATAG
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>LIP05short_R
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CCTTAGCTCTTTTCTTTTGT
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>LIP06short_F
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GAAGGAAGGAAGCAATTATT
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>LIP06short_R
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TGACTTACCCTTTTTACCTT
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>LIP07short_F
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CACATGTTTGTCACTCTAAT
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>LIP07short_R
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GAAGTGAGGCCTAAAATAAA
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>LIP08short_F
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GAATGTATTGTCTTTGATCC
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>LIP08short_R
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GTTGGATTTTGTTCTTTCCA
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>LIP09short_F
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AGAAAAACGTCGATACCAAA
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>LIP09short_R
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CGATTTAGTAACCTTAGAAC
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>LIP10short_F
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ATCTTCAAAATGTCTCTAGG
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>LIP10short_R
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TACAGATATTCTTAGGCAGT
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>LIP11short_F
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TGTAACTCTCAATTAAGCAG
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>LIP11short_R
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ATCTTTCTGTAAGCACTTAG
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>LIP12short_F
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CTAGAACCGATTTGTTCAAA
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>LIP12short_R
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GCAGTTGTTTTGGATTAACA
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>LIP13short_F
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AAAGAGAAAGCAGAGAAATC
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>LIP13short_R
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ATGTATAGATTGGAGGAAAG
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>LIP14short_F
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ATTATGGAAAGGAATTGGAG
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>LIP14short_R
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CCATGTCTAGTATTTACTCA
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>LIP15short_F
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TTAATGACTGATCGTTAGTG
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>LIP15short_R
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CGGGAGTTATGAAAAATAGT
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>LIP24short_F
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AGTATGGTTTCAACATATGG
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>LIP24short_R
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GATATGAAGTTGACATGCTA
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>LIP16short_F
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ATTTAAAAGCTCGTAACTCC
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>LIP16short_R
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GGATAAGCAATTACAACACA
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>LIP17short_F
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CCCAAATTTTTAAATGCACC
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>LIP17short_R
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CTCTTGGAACGTGAAAAATT
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>LIP18short_F
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TTTTCTAGAAGGATTTGTGC
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>LIP18short_R
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CCATGCAAACCCAATTTTAA
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>LIP19short_F
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GTAAAACTAAGGTTGAGCTA
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>LIP19short_R
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CCACAAGTCACAACAATTTA
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>LIP20short_F
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TTATTTGTATGTTGGAGACC
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>LIP20short_R
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CATGGTATATAGGTTTAGGT
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>LIP21short_F
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CATAGAGAGTTTTGGATTAC
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>LIP21short_R
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AAAGAACTGATAGTGTCATG
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>LIP22short_F
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ATATGTACATGTATGGTGTG
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>LIP22short_R
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CCTAAATCTAGCAGAAGATT
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>LIP23short_F
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ATGTATGGAGAAATGGGTTA
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>LIP23short_R
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ATATAGAAATGGAGGTTGCT
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(listed in BACKUP(J:)/박사/Indel Candidate/LIP_short_primer.fa)
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Latest revision as of 02:22, 18 December 2017

2017 Jan Taeyoung Lab note

2017 Feb Taeyoung Lab note

2017 Mar Taeyoung Lab note

2017 May Taeyoung Lab note

2017 Sep Taeyoung Lab note

2017 Oct Taeyoung Lab note

2017 Nov Taeyoung Lab note

2017 Dec Taeyoung Lab note