From Crop Genomics Lab.
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− | == 2017 1.2 ==
| + | [[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 ====
| + | [[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) ====
| + | [[2017 Mar Taeyoung Lab note]] |
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| + | [[2017 May Taeyoung Lab note]] |
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− | ==== KaKs calculation using scripts provided by MCscanX ====
| + | [[2017 Sep Taeyoung Lab note]] |
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− | '''KaKs calculation between Jatropha species'''
| + | [[2017 Oct Taeyoung Lab note]] |
− | 244 :python /alima9002/63_backup/Jatropha/CDS/run.kaks.py
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− | ==== LIP short primer preparation ====
| + | [[2017 Nov Taeyoung Lab note]] |
− | ===== Primer info =====
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− | >LIP01short_F
| + | [[2017 Dec Taeyoung Lab note]] |
− | 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