Difference between revisions of "2017 Feb Taeyoung Lab note"
From Crop Genomics Lab.
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python ~/py/LIP/6-1.manual_primer_design.py CS-14-contigs.fa.blastn.single_type.blastn.indel_candidates.read_evidence ../../CS-14/qvalue/CS-14-contigs.fa > CS-14.short.primer.fa.2candidates | python ~/py/LIP/6-1.manual_primer_design.py CS-14-contigs.fa.blastn.single_type.blastn.indel_candidates.read_evidence ../../CS-14/qvalue/CS-14-contigs.fa > CS-14.short.primer.fa.2candidates | ||
+ | |||
+ | ==2017.2.8~2.10== | ||
+ | Field work | ||
+ | |||
+ | ==2017.2.13== | ||
+ | ===LIPs-13 and 16 re-design=== | ||
+ | python ~/py/LIP/6-1.manual_primer_design.py CS-14-contia.blastn.single_type.blastn.indel_candidates.read_evidence ../../CS-14/qvalue/CS-14-contigs.fa > CS-14.short.primer.fa.2candidates | ||
+ | ===e-PCR=== | ||
+ | re-PCR -S ../../CS-14/qvalue/CS-14-contigs.hash -n1 -g1 CS-14.short.primer.fa.2candidates.sts -o CS-14.short.primer.fa.2candidates.sts.out | ||
+ | ===Primer order=== | ||
+ | ===OrthoMcl of Jatropha organ=== | ||
+ | all done | ||
+ | ===Draw venn diagram using Jatropha organ data=== | ||
+ | require(Vennerable) | ||
+ | Data <- read.table("group.txt.binary.parsed.rawinput.endosperm",col.names="") | ||
+ | Organ <- c("SG","LG","Y","B") | ||
+ | png(filename="Venn.endosperm.png",width=2000,height=2000) | ||
+ | plot(Venn(SetNames=Organ,Weight=as.vector(Data$X)),doWeights=F,type="ellipses") | ||
+ | dev.off() | ||
+ | ===OrthoMcl of Jatropha species=== | ||
+ | Pairs done |
Revision as of 06:46, 13 February 2017
Contents |
2017.2.2
PCR with LIP short primer
Ladder, 1-wild,1-cultivated,2-wild,2-cultivated order
LIP01-24
Last 4 bands are Tubulin control in CS-12,CS-14,KS-04,W82
1% agar, 100V, 1h, Tm:56,
2017.2.3
PCR with LIP short primer
Ladder, 1-wild,1-cultivated,2-wild,2-cultivated order
SLIP01,02,03,06,07,09,13,14,15,16,20,24
Last 3 bands are Tubulin control in CS-12,CS-14,W82
1% agar, 100V, 1h, Tm:56,
2017.2.6
PCR with LIP short primer
Ladder, 1-wild,1-cultivated,2-wild,2-cultivated order
SLIP01,02,03,06,07,13,14,15,16,20,24
Last 3 bands are Tubulin control in CS-12,CS-14,W82
1% agar, 100V, 1h, Tm:56,
2017.2.7
PCR with LIP short primer
Ladder, 1-wild,1-cultivated,2-wild,2-cultivated order
2017.02.07 SLIP-08,12,13,20 with Wild and W82
Last 3 bands are Tubulin control in CS-12,CS-14,W82
1% agar, 100V, 1h, Tm:56,
Primer re-design
SLIP-13 and 16 is re-designed
python ~/py/LIP/6-1.manual_primer_design.py CS-14-contigs.fa.blastn.single_type.blastn.indel_candidates.read_evidence ../../CS-14/qvalue/CS-14-contigs.fa > CS-14.short.primer.fa.2candidates
2017.2.8~2.10
Field work
2017.2.13
LIPs-13 and 16 re-design
python ~/py/LIP/6-1.manual_primer_design.py CS-14-contia.blastn.single_type.blastn.indel_candidates.read_evidence ../../CS-14/qvalue/CS-14-contigs.fa > CS-14.short.primer.fa.2candidates
e-PCR
re-PCR -S ../../CS-14/qvalue/CS-14-contigs.hash -n1 -g1 CS-14.short.primer.fa.2candidates.sts -o CS-14.short.primer.fa.2candidates.sts.out
Primer order
OrthoMcl of Jatropha organ
all done
Draw venn diagram using Jatropha organ data
require(Vennerable) Data <- read.table("group.txt.binary.parsed.rawinput.endosperm",col.names="") Organ <- c("SG","LG","Y","B") png(filename="Venn.endosperm.png",width=2000,height=2000) plot(Venn(SetNames=Organ,Weight=as.vector(Data$X)),doWeights=F,type="ellipses") dev.off()
OrthoMcl of Jatropha species
Pairs done