Difference between revisions of "2017 Taeyoung Lab note"

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(2017 1.2)
(Ongoing)
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== 2017 1.2 ==
 
== 2017 1.2 ==
==== 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
 
 
== Ongoing ==
 
 
==== Jatropha transcriptome Trinity assemble ====
 
==== Jatropha transcriptome Trinity assemble ====
 
  raw data : 244:/NGS/NGS/JatrophaCurcas/RNA
 
  raw data : 244:/NGS/NGS/JatrophaCurcas/RNA

Revision as of 07:14, 3 January 2017

Contents

2017 1.2

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

SNP typing among IT182932,IT1099098,Hwangkeum-Kong

1.Read mapping using bwa mem with default options (/home/hayasen/Workspace/Glycine/GlycineMax/ver275/Reads/)

2.mpileup

samtools mpileup -f /alima9002/ref/Gmax/assembly/Gmax_275_v2.0.fa -v -t DP,AD,ADF,ADR,SP,INFO/AD,INFO/ADF,INFO/ADR -u -b bam_list | bcftools call -v -m -O v > Variant.vcf

LIP short primer gradient PCR

1~8 primer is tested with CS-12 Gradiant lower temp is 50 upper temp is 65