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]] |
− | 244:python vcf.parsing.for.mandf.py UV.vcf.SNPonly 3 0.01 except_sample.txt > UV.vcf.SNPonly.except.LowDepthSample.d3.Q30.m0.1.loc
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− | loc file is manually edited by excel
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− | Genetic map is constructed using Joinmap 4.1
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− | ==== KaKs calculation using scripts provided by MCscanX ====
| + | [[2017 May Taeyoung Lab note]] |
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− | '''KaKs calculation between Jatropha species'''
| + | [[2017 Sep Taeyoung Lab note]] |
− | 244 :python /alima9002/63_backup/Jatropha/CDS/run.kaks.py
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− | ==== Large Insertion Prediction ====
| + | [[2017 Oct Taeyoung Lab note]] |
− | ===== LIP short primer preparation =====
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− | '''Primer info'''
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− | >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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− | Primer dilution
| + | [[2017 Nov Taeyoung Lab note]] |
| + | |
| + | [[2017 Dec Taeyoung Lab note]] |
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