Rahul Nayak
A Bioinformatician
Our Sponsors
Estimate Genome Size with Jellyfish and R
By Rahul Nayak 2447 days ago Comments (1)
jellyfish count -t 8 -C -m 19 -s 5G -o 19mer_out --min-qual-char=? /common/Tutorial/Genome_estimation/sample_read_1.fastq /common/Tutorial/Genome_estimation/sample_read_2.fastq
#-t -treads=unit32 Number of treads to be used in the run. eg: 1,2,3,..etc.
#-C -both-strands Count both strands
#-m -mer-len=unit32 Length of the k-mer
#-s -size=unit32 Hash size / memory allocation
#-o -output=string Output file name
#--min-quality-char Base quality value. Version 2.2.3 of Jellyfish uses the “Phred” score, where "?" = 30
jellyfish histo -o 19mer_out.histo 19mer_out
#Plot
dataframe19 <- read.table("19mer_out.histo") #load the data into dataframe19
plot(dataframe19[1:200,], type="l") #plots the data points 1 through 200 in the dataframe19 using a line
plot(dataframe19[2:200,], type="l")
plot(dataframe19[2:100,], type="l") #plot line graph
points(dataframe19[2:100,]) #plot the data points from 2 through 100
sum(as.numeric(dataframe19[2:9325,1]*dataframe19[2:9325,2]))
data[10:20,]
sum(as.numeric(dataframe19[2:9325,1]*dataframe19[2:9325,2]))/12
#Return around ~ 305 Mb
Comments
Jellyfish manual at http://www.genome.umd.edu/docs/JellyfishUserGuide.pdf