pbglmichaelhall / fastq

FASTQ

Prerequisite software

apt install sra-toolkit

To retreive FASTQ use SRA toolkit and NCBI database. Go to https://www.ncbi.nlm.nih.gov/sra

There is one Result

Click of the Hyperlink

Look at the Metadata

It matches linux command line standard output:

The Data Tree after G Zipping the FASTA File

The Following R Package "fastqcr" can analyze a FASTQ sample like this one or multiple FASTQ files

setwd("/home/michael/Desktop/SRA")
install.packages("fastqcr")
library(fastqcr)
fastqc_install()
fastqc(fq.dir = "/home/michael/Desktop/SRA/FASTQ",threads = 4)

THe new Data Tree

# 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")

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")

ERROR

If we want to convert a FASTQ file to a FASTA file then the following command should be adequate