Difference between revisions of "2017 Taeyoung Lab note"
From Crop Genomics Lab.
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244 :python /alima9002/63_backup/Jatropha/CDS/run.kaks.py | 244 :python /alima9002/63_backup/Jatropha/CDS/run.kaks.py | ||
+ | |||
+ | ==== LIP short primer preparation ==== | ||
+ | ===== Primer info ===== | ||
+ | >LIP01short_F | ||
+ | AACTGAACACAGACAATGAA | ||
+ | >LIP01short_R | ||
+ | CAATTTATACACCACCTTAC | ||
+ | >LIP02short_F | ||
+ | CTCTTTGTATTTGGTGACAA | ||
+ | >LIP02short_R | ||
+ | GTATTAGCAGCTTTTGCTTA | ||
+ | >LIP03short_F | ||
+ | AATTGTAAGACATATCCCTC | ||
+ | >LIP03short_R | ||
+ | CTGCCCCACTAATAATTAAT | ||
+ | >LIP04short_F | ||
+ | TAAAAACAGAACTTGTCCAC | ||
+ | >LIP04short_R | ||
+ | ATCACAAGACTGAACAAGTA | ||
+ | >LIP05short_F | ||
+ | ATTGACATAAGGTTGCATAG | ||
+ | >LIP05short_R | ||
+ | CCTTAGCTCTTTTCTTTTGT | ||
+ | >LIP06short_F | ||
+ | GAAGGAAGGAAGCAATTATT | ||
+ | >LIP06short_R | ||
+ | TGACTTACCCTTTTTACCTT | ||
+ | >LIP07short_F | ||
+ | CACATGTTTGTCACTCTAAT | ||
+ | >LIP07short_R | ||
+ | GAAGTGAGGCCTAAAATAAA | ||
+ | >LIP08short_F | ||
+ | GAATGTATTGTCTTTGATCC | ||
+ | >LIP08short_R | ||
+ | GTTGGATTTTGTTCTTTCCA | ||
+ | >LIP09short_F | ||
+ | AGAAAAACGTCGATACCAAA | ||
+ | >LIP09short_R | ||
+ | CGATTTAGTAACCTTAGAAC | ||
+ | >LIP10short_F | ||
+ | ATCTTCAAAATGTCTCTAGG | ||
+ | >LIP10short_R | ||
+ | TACAGATATTCTTAGGCAGT | ||
+ | >LIP11short_F | ||
+ | TGTAACTCTCAATTAAGCAG | ||
+ | >LIP11short_R | ||
+ | ATCTTTCTGTAAGCACTTAG | ||
+ | >LIP12short_F | ||
+ | CTAGAACCGATTTGTTCAAA | ||
+ | >LIP12short_R | ||
+ | GCAGTTGTTTTGGATTAACA | ||
+ | >LIP13short_F | ||
+ | AAAGAGAAAGCAGAGAAATC | ||
+ | >LIP13short_R | ||
+ | ATGTATAGATTGGAGGAAAG | ||
+ | >LIP14short_F | ||
+ | ATTATGGAAAGGAATTGGAG | ||
+ | >LIP14short_R | ||
+ | CCATGTCTAGTATTTACTCA | ||
+ | >LIP15short_F | ||
+ | TTAATGACTGATCGTTAGTG | ||
+ | >LIP15short_R | ||
+ | CGGGAGTTATGAAAAATAGT | ||
+ | >LIP24short_F | ||
+ | AGTATGGTTTCAACATATGG | ||
+ | >LIP24short_R | ||
+ | GATATGAAGTTGACATGCTA | ||
+ | >LIP16short_F | ||
+ | ATTTAAAAGCTCGTAACTCC | ||
+ | >LIP16short_R | ||
+ | GGATAAGCAATTACAACACA | ||
+ | >LIP17short_F | ||
+ | CCCAAATTTTTAAATGCACC | ||
+ | >LIP17short_R | ||
+ | CTCTTGGAACGTGAAAAATT | ||
+ | >LIP18short_F | ||
+ | TTTTCTAGAAGGATTTGTGC | ||
+ | >LIP18short_R | ||
+ | CCATGCAAACCCAATTTTAA | ||
+ | >LIP19short_F | ||
+ | GTAAAACTAAGGTTGAGCTA | ||
+ | >LIP19short_R | ||
+ | CCACAAGTCACAACAATTTA | ||
+ | >LIP20short_F | ||
+ | TTATTTGTATGTTGGAGACC | ||
+ | >LIP20short_R | ||
+ | CATGGTATATAGGTTTAGGT | ||
+ | >LIP21short_F | ||
+ | CATAGAGAGTTTTGGATTAC | ||
+ | >LIP21short_R | ||
+ | AAAGAACTGATAGTGTCATG | ||
+ | >LIP22short_F | ||
+ | ATATGTACATGTATGGTGTG | ||
+ | >LIP22short_R | ||
+ | CCTAAATCTAGCAGAAGATT | ||
+ | >LIP23short_F | ||
+ | ATGTATGGAGAAATGGGTTA | ||
+ | >LIP23short_R | ||
+ | ATATAGAAATGGAGGTTGCT | ||
+ | (listed in BACKUP(J:)/박사/Indel Candidate/LIP_short_primer.fa) |
Revision as of 04:50, 2 January 2017
Contents |
2017 1.2
Ongoing
Jatropha transcriptome Trinity assemble
raw data : 244:/NGS/NGS/JatrophaCurcas/RNA Jatropha species transcriptome assemble : Jct,Jcu, Jin, Jgo, Jci, Jpo, Jmu, Jma, Jac, Rco (listed in 244:/NGS/NGS/JatrophaCurcas/RNA/list). All done Jatropha organ transcriptome assemble : Leaf, Root, Stem, Female flower, Male flower, LG, SG, Y, B. All done
Cdhit
193:/data2/alima90/program/cdhit/cd-hit -i Y.cds.fa -M 10000 -o Y.cds.fa.cdhit -T 5 193:/data2/alima90/program/cdhit/cd-hit -i LG.cds.fa -M 10000 -o LG.cds.fa.cdhit -T 5
UV GBS mapping (w/ joinmap)
KaKs calculation using scripts provided by MCscanX
244 :python /alima9002/63_backup/Jatropha/CDS/run.kaks.py
LIP short primer preparation
Primer info
>LIP01short_F AACTGAACACAGACAATGAA >LIP01short_R CAATTTATACACCACCTTAC >LIP02short_F CTCTTTGTATTTGGTGACAA >LIP02short_R GTATTAGCAGCTTTTGCTTA >LIP03short_F AATTGTAAGACATATCCCTC >LIP03short_R CTGCCCCACTAATAATTAAT >LIP04short_F TAAAAACAGAACTTGTCCAC >LIP04short_R ATCACAAGACTGAACAAGTA >LIP05short_F ATTGACATAAGGTTGCATAG >LIP05short_R CCTTAGCTCTTTTCTTTTGT >LIP06short_F GAAGGAAGGAAGCAATTATT >LIP06short_R TGACTTACCCTTTTTACCTT >LIP07short_F CACATGTTTGTCACTCTAAT >LIP07short_R GAAGTGAGGCCTAAAATAAA >LIP08short_F GAATGTATTGTCTTTGATCC >LIP08short_R GTTGGATTTTGTTCTTTCCA >LIP09short_F AGAAAAACGTCGATACCAAA >LIP09short_R CGATTTAGTAACCTTAGAAC >LIP10short_F ATCTTCAAAATGTCTCTAGG >LIP10short_R TACAGATATTCTTAGGCAGT >LIP11short_F TGTAACTCTCAATTAAGCAG >LIP11short_R ATCTTTCTGTAAGCACTTAG >LIP12short_F CTAGAACCGATTTGTTCAAA >LIP12short_R GCAGTTGTTTTGGATTAACA >LIP13short_F AAAGAGAAAGCAGAGAAATC >LIP13short_R ATGTATAGATTGGAGGAAAG >LIP14short_F ATTATGGAAAGGAATTGGAG >LIP14short_R CCATGTCTAGTATTTACTCA >LIP15short_F TTAATGACTGATCGTTAGTG >LIP15short_R CGGGAGTTATGAAAAATAGT >LIP24short_F AGTATGGTTTCAACATATGG >LIP24short_R GATATGAAGTTGACATGCTA >LIP16short_F ATTTAAAAGCTCGTAACTCC >LIP16short_R GGATAAGCAATTACAACACA >LIP17short_F CCCAAATTTTTAAATGCACC >LIP17short_R CTCTTGGAACGTGAAAAATT >LIP18short_F TTTTCTAGAAGGATTTGTGC >LIP18short_R CCATGCAAACCCAATTTTAA >LIP19short_F GTAAAACTAAGGTTGAGCTA >LIP19short_R CCACAAGTCACAACAATTTA >LIP20short_F TTATTTGTATGTTGGAGACC >LIP20short_R CATGGTATATAGGTTTAGGT >LIP21short_F CATAGAGAGTTTTGGATTAC >LIP21short_R AAAGAACTGATAGTGTCATG >LIP22short_F ATATGTACATGTATGGTGTG >LIP22short_R CCTAAATCTAGCAGAAGATT >LIP23short_F ATGTATGGAGAAATGGGTTA >LIP23short_R ATATAGAAATGGAGGTTGCT (listed in BACKUP(J:)/박사/Indel Candidate/LIP_short_primer.fa)