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− | == Ongoing ==
| + | [[2017 Jan Taeyoung Lab note]] |
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− | 1. Variant calling among HGK, IT182932, IT109098
| + | [[2017 Feb Taeyoung Lab note]] |
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− | 2. Cdhit
| + | [[2017 Mar Taeyoung Lab note]] |
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− | 3. Gradiant PCR using LIP short primer
| + | [[2017 May Taeyoung Lab note]] |
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| + | [[2017 Sep Taeyoung Lab note]] |
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− | == 2017 1.2 ==
| + | [[2017 Oct Taeyoung Lab note]] |
− | ==== Jatropha transcriptome Trinity assemble ====
| + | |
− | 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 Nov 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 Dec 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 ====
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− | | + | |
− | '''KaKs calculation between Jatropha species'''
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− | 244 :python /alima9002/63_backup/Jatropha/CDS/run.kaks.py
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− | | + | |
− | ==== Large Insertion Prediction ====
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− | ===== 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
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− | | + | |
− | == 2017. 1. 3 ==
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− | ===AMORE work===
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− | | + | |
− | python ~/py/ret_fasta_by_gene_name.py /alima9002/ref/Athaliana/annotation/Athaliana_167_TAIR10.cds.fa gene_list.txt > gene_list.txt.fa
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− | 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
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− | | + | |
− | '''Homolog with Ath'''
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− | Glyma.08G014900
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− | Glyma.05G208300
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− | Glyma.20G001900
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− | Glyma.03G176600
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− | Glyma.19G177400
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− | Glyma.03G262600
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− | Glyma.06G202300
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− | Glyma.05G021800
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− | Glyma.17G077700
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− | Glyma.05G022000
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− | Glyma.09G234900
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− | Glyma.19G025000
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− | Glyma.10G224000
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− | Glyma.02G081000
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− | Glyma.20G167800
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− | Glyma.14G072700
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− | Glyma.17G252200
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− | Glyma.17G050500
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− | Glyma.07G038000
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− | Glyma.13G109100
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− | Glyma.16G007200
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− | Glyma.19G105100
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− | Glyma.09G283800
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− | Glyma.20G172700
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− | Glyma.02G076300
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− | | + | |
− | '''SNP typing among IT182932,IT1099098,Hwangkeum-Kong'''
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− | | + | |
− | 1.Read mapping using bwa mem with default options (/home/hayasen/Workspace/Glycine/GlycineMax/ver275/Reads/)
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− | | + | |
− | 2.mpileup
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− | 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
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− | | + | |
− | ===LIP short primer gradient PCR===
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− | 1~8 primer is tested with CS-12
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− | | + | |
− | Gradiant lower temp is 50 upper temp is 65
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− | | + | |
− | Sample is loaded on 1% agarose gel and It was run with 100 V on 1 hour.
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− | | + | |
− | {| class="wikitable"
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− | |-
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− | | 52.7 || 54.1 || 55.5 || 56.8 || 58.2 | 59.5 || 60.9 || 62.3
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− | |}
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− | | + | |
− | <gallery>
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− | File:17010301.jpeg|LIPshort01-04
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− | </gallery>
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− | 1 2
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− | 3 4
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− | LIPshort1 -> Error when it is loaded
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− | | + | |
− | LIPshort4 -> 55.5~59.5에서 증폭한 샘플만 로딩
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− | | + | |
− | <gallery>
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− | File:17010302.jpg|Caption2
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− | </gallery>
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− | 5 6
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− | 7 8
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− | Estimated Tm:55.5~56.8
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− | | + | |
− | | + | |
− | == 2017.1.4~2017.1.6 ==
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− | | + | |
− | 농장 출장
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− | | + | |
− | == 2017.1.9 ==
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− | | + | |
− | ===AMORE(GK, IT182932, IT109098)===
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− | ==== VCF parsing ====
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− | python ~/py/Reseq/filter.vcf.by.phred.hetero.depth.py Variant.vcf.SNP 5 > Variant.vcf.SNP.filtered.d5.Q30.homo
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− | ==== Typing ====
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− | cat Variant.vcf.SNP.filtered.d5.Q30.homo.diff | python ~/py/Reseq/[Reseq]SNP_counter.py /alima9002/ref/Gmax/annotation/Gmax_275_Wm82.a2.v1.gene_exons.gff3 /alima9002/ref/Gmax/assembly/Gmax_275_v2.0.fa 30 > Variant.vcf.SNP.filtered.d5.Q30.homo.diff.type
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− | | + | |
− | ===Jatropha OrthoMcl===
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− | Retrieve complete pep only for OrthoMcl
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− | | + | |
− | == 2017.1.10 ==
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− | ===AMORE(GK, IT182932, IT109098)===
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− | ==== filtering SNPs on homologous ====
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− | python ret_homolog_only.py Variant.vcf.SNP.filtered.d5.Q30.homo.diff.type homologs.txt > Variant.vcf.SNP.filtered.d5.Q30.homo.diff.type.homologs.only
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− | ==== Syn or Nonsyn typing ====
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− | python ~/py/Reseq/\[Reseq\]det_syn.py /alima9002/ref/Gmax/annotation/Gmax_275_Wm82.a2.v1.gene_exons.gff3 /alima9002/ref/Gmax/assembly/Gmax_275_v2.0.fa Variant.vcf.SNP.filtered.d5.Q30.homo.diff.type.homologs.only.CDS > Variant.vcf.SNP.filtered.d5.Q30.homo.diff.type.homologs.only.CDS.SynNonsyn
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− | ===Lactuca Indica Cdhit===
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− | /alima9002/program/cd-hit-v4.6.4-2015-0603/cd-hit -i L.Trinity.fasta -o L.Trinity.fasta.cdhit -T 10 -M 10000
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− | == 2017.1.11==
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− | 농장 출장
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− | | + | |
− | == 2017.1.12==
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− | ===Amore===
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− | ====Make SNP tables====
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− | ====INDEL analysis using snpEff====
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− | java -jar /alima9002/program/snpEff/snpEff.jar ann -c /alima9002/program/snpEff/snpEff.config gmax275 Variant.vcf.INDEL > Variant.vcf.INDEL.snpEff
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− | ==== homologs filtering using annotation file ====
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− | ==== VCF filter by homologs retrieved by ann file ====
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− | python ret_homolog_only.py Variant.vcf.SNP.filtered.d5.Q30.homo.diff.type homologs.by.ann.txt > Variant.vcf.SNP.filtered.d5.Q30.homo.diff.type.hom.ann
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− | ==== Determination Synonymous ====
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− | python ~/py/Reseq/\[Reseq\]det_syn.py /alima9002/ref/Gmax/annotation/Gmax_275_Wm82.a2.v1.gene_exons.gff3 /alima9002/ref/Gmax/assembly/Gmax_275_v2.0.fa Variant.vcf.SNP.filtered.d5.Q30.homo.diff.type.hom.ann.CDS > Variant.vcf.SNP.filtered.d5.Q30.homo.diff.type.hom.ann.CDS.SynNonsyn
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