apt install sra-toolkit
To retreive FASTQ use SRA toolkit and NCBI database. Go to https://www.ncbi.nlm.nih.gov/sra
setwd("/home/michael/Desktop/SRA")
install.packages("fastqcr")
library(fastqcr)
fastqc_install()
fastqc(fq.dir = "/home/michael/Desktop/SRA/FASTQ",threads = 4)
# Generating fastqc file automatically makes a FASTQC directory
qc.file <- "/home/michael/Desktop/SRA/FASTQ/FASTQC/SRR2121685_fastqc.zip"
#Read fastqc file
qc <- qc_read(qc.file)
#Produce Names
names(qc)
#Plotting
qc_plot(qc, "summary")
qc_plot(qc, "Basic statistics")
qc_plot(qc, "Per base sequence quality")
qc_plot(qc, "Per base sequence content")
qc_plot(qc, "Per sequence GC content")
qc_plot(qc, "Per sequence quality scores")
qc_plot(qc, "Sequence duplication levels")
qc_plot(qc, "Per base N content")
qc_plot(qc, "Sequence length distribution")
qc_plot(qc, "Sequence duplication levels")
qc_plot(qc, "Overrepresented sequences")
qc_plot(qc, "Adapter content")
qc_plot(qc, "Kmer content")