Difference between revisions of "2017 Feb Taeyoung Lab note"

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(PCR with LIP short primer)
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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
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==2017.2.8~2.10==
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Field work
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==2017.2.13==
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===LIPs-13 and 16 re-design===
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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
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===e-PCR===
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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
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===Primer order===
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===OrthoMcl of Jatropha organ===
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all done
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===Draw venn diagram using Jatropha organ data===
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require(Vennerable)
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Data <- read.table("group.txt.binary.parsed.rawinput.endosperm",col.names="")
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Organ <- c("SG","LG","Y","B")
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png(filename="Venn.endosperm.png",width=2000,height=2000)
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plot(Venn(SetNames=Organ,Weight=as.vector(Data$X)),doWeights=F,type="ellipses")
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dev.off()
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===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