Difference between revisions of "2017 Taeyoung Lab note"
From Crop Genomics Lab.
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== 2017. 1. 3 == | == 2017. 1. 3 == | ||
+ | ===AMORE work=== | ||
+ | python ~/py/ret_fasta_by_gene_name.py /alima9002/ref/Athaliana/annotation/Athaliana_167_TAIR10.cds.fa gene_list.txt > gene_list.txt.fa |
Revision as of 05:25, 3 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)
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 loc file is manually edited by excel Genetic map is constructed using Joinmap 4.1
KaKs calculation using scripts provided by MCscanX
KaKs calculation between Jatropha species 244 :python /alima9002/63_backup/Jatropha/CDS/run.kaks.py
Large Insertion Prediction
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)
Primer dilution
2017. 1. 3
AMORE work
python ~/py/ret_fasta_by_gene_name.py /alima9002/ref/Athaliana/annotation/Athaliana_167_TAIR10.cds.fa gene_list.txt > gene_list.txt.fa