Difference between revisions of "2017 Feb Taeyoung Lab note"

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  dev.off()
 
  dev.off()
 
===OrthoMcl of Jatropha species===
 
===OrthoMcl of Jatropha species===
Pairs done
+
all done
 +
 
 +
===Drawing venn diagram using Jatropha species data===
 +
done
 +
 
 +
===BLASTP for Ks calculation among Jatropha species===
 +
193:/data2/alima90/Jatropha/KaKs_nocdhit$python blastp.py  # blastp -db Jct.cds.fa.pep.complete.fa -evalue 1e-10 -outfmt 6 -num_threads 20 -num_alignments 5 -query Rco.cds.fa.pep.complete.fa -out Jct.Rco.blastp.1e-10.na5.outfmt6
 +
 
 +
==2017.2.20==
 +
[[File:2017022001.jpg|frameless|LIPs-13a,16a with CS-14 and W82 Tm:56 1% agar 130ml gel 100v 1h]]
 +
 
 +
LIPs-13a,16a with CS-14 and W82
 +
 
 +
Tm:56
 +
 
 +
1% agar 130ml gel 100v 1h
 +
 
 +
==2017.2.22==
 +
===LIPs PCR===
 +
[[File:2017022201.jpg|frameless|2017.2.22 LIPs-13a Gradient using CS-14 and W82 Tm:50-65 130ml gel 1% Agar 100v 1h]]
 +
 
 +
LIPs-13a Gradient using CS-14 and W82
 +
 
 +
Tm:50-65
 +
 
 +
130ml gel
 +
 
 +
1% Agar 100v 1h
 +
 
 +
===Muay GBS filtering and mapping===
 +
python run_trimming.py
 +
python run_mapping.py
 +
 
 +
===KaKs calculation using Jatropha species transcriptome===
 +
====retrieve common gene between blastp and orthomcl in nocdhit result====
 +
/alima9002/63_backup/Jatropha/CDS/KaKs_nocdhit : python ret_common_gene_between_groups_and_blastp.py Jct.Jac.blastp.1e-10.na5.outfmt6 groups.txt Jct.Jac.blastp.1e-10.na5.outfmt6.grouped
 +
====KaKs calculation using genes from blastp only====
 +
/alima9002/63_backup/Jatropha/CDS/KaKs_only_blast : python run.kaks.py

Latest revision as of 07:57, 22 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

all done

Drawing venn diagram using Jatropha species data

done

BLASTP for Ks calculation among Jatropha species

193:/data2/alima90/Jatropha/KaKs_nocdhit$python blastp.py   # blastp -db Jct.cds.fa.pep.complete.fa -evalue 1e-10 -outfmt 6 -num_threads 20 -num_alignments 5 -query Rco.cds.fa.pep.complete.fa -out Jct.Rco.blastp.1e-10.na5.outfmt6

2017.2.20

LIPs-13a,16a with CS-14 and W82 Tm:56 1% agar 130ml gel 100v 1h

LIPs-13a,16a with CS-14 and W82

Tm:56

1% agar 130ml gel 100v 1h

2017.2.22

LIPs PCR

2017.2.22 LIPs-13a Gradient using CS-14 and W82 Tm:50-65 130ml gel 1% Agar 100v 1h

LIPs-13a Gradient using CS-14 and W82

Tm:50-65

130ml gel

1% Agar 100v 1h

Muay GBS filtering and mapping

python run_trimming.py
python run_mapping.py

KaKs calculation using Jatropha species transcriptome

retrieve common gene between blastp and orthomcl in nocdhit result

/alima9002/63_backup/Jatropha/CDS/KaKs_nocdhit : python ret_common_gene_between_groups_and_blastp.py Jct.Jac.blastp.1e-10.na5.outfmt6 groups.txt Jct.Jac.blastp.1e-10.na5.outfmt6.grouped

KaKs calculation using genes from blastp only

/alima9002/63_backup/Jatropha/CDS/KaKs_only_blast : python run.kaks.py