https://bioinformaticsonline.com/snippets/view/35910/estimate-genome-size-with-jellyfish-and-r? https://bioinformaticsonline.com/snippets/view/35910/estimate-genome-size-with-jellyfish-and-r Mon, 12 Mar 2018 10:11:19 -0500 https://bioinformaticsonline.com/snippets/view/35910/estimate-genome-size-with-jellyfish-and-r 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]]> Rahul Nayak https://bioinformaticsonline.com/snippets/view/35910/estimate-genome-size-with-jellyfish-and-r#item-annotation-3986 Sat, 28 Aug 2021 03:48:03 -0500 https://bioinformaticsonline.com/snippets/view/35910/estimate-genome-size-with-jellyfish-and-r#item-annotation-3986 Jellyfish manual at http://www.genome.umd.edu/docs/JellyfishUserGuide.pdf

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