Difference between revisions of "2017 Taeyoung Lab note"

Revision as of 07:02, 3 January 2017

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
blastp -db /alima9002/ref/Gmax/annotation/Gmax_275_Wm82.a2.v1.protein.fa -query gene_list.txt.pep.fa -evalue 1e-5 -num_alignments 1 -outfmt 6 -num_threads 6 -out gene_list.txt.pep.fablastp.Gm275.1e-5.out6

Homolog with Ath Glyma.08G014900 Glyma.05G208300 Glyma.20G001900 Glyma.03G176600 Glyma.19G177400 Glyma.03G262600 Glyma.06G202300 Glyma.05G021800 Glyma.17G077700 Glyma.05G022000 Glyma.09G234900 Glyma.19G025000 Glyma.10G224000 Glyma.02G081000 Glyma.20G167800 Glyma.14G072700 Glyma.17G252200 Glyma.17G050500 Glyma.07G038000 Glyma.13G109100 Glyma.16G007200 Glyma.19G105100 Glyma.09G283800 Glyma.20G172700 Glyma.02G076300