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Commit e98ba5f6 authored by Evert Van-Schaik's avatar Evert Van-Schaik
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1 merge request!5Evert.van schaik master patch 96224
simka 0 → 100644
# creates liste of the samples.
ls *subset* > temp
#creates right format for SIMKA
awk -v var=$(pwd) '{print "id"NR": "var"/"$0}' temp > liste
conda activate simka-1.5.2
### Kmersize can be optimized for the sample, default is 21, tmp files can be kept, but is not necessary.
[location]/bin/simka -in [liste] -out simka_out -out-tmp simka_temp -keep-tmp -kmer-size 30 -nb-cores 4 -max-reads [number]
### R script to make figure
### REMOVE FIRST ; IN CSV FILES!!!!
a<-as.matrix(read.table("file.csv",sep=";",header=T))
#list
rownames(a)<- c("samplename1","samplename2")
colnames(a)<- c("samplename1","samplename2")
#plot
heatmap(a,trace="none", Rowv=F)
#print plot
pdf("name.pdf", width=15, height=15)
heatmap(a,trace="none", Rowv=F)
dev.off()
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