https://www.ncbi.nlm.nih.gov/guide/howto/dwn-genome/
fastq-dump ERR4835478
setwd("/home/michael/Desktop/Alignment")
install.packages("fastqcr")
library(fastqcr)
fastqc_install()
fastqc(fq.dir = "/home/michael/Desktop/Alignment/FASTQ",threads = 4)
qc.file <- "/home/michael/Desktop/Alignment/FASTQ/FASTQC/ERR4835478_fastqc.zip"
qc <- qc_read(qc.file)
names(qc)
#These commands are only necessary to plot in RStudio Viewer, otherwise the most important plots are automatically genearted to HTML file in FASTQC directory
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")
setwd("/home/michael/Desktop/Alignment/plots")
library(QTLseqr)
library(tinytex)
library(vcfR)
library(tidyr)
library(ggplot2)
library(dplyr)
library(ggrepel)
library(ggpubr)
library(data.table)
# Define a vector of Chromosomes
Chroms <- c("NC_016131.3","NC_016132.3","NC_016133.3","NC_016134.3","NC_016135.3")
file <- "vcfnewsamplename.vcf.gz"
QTLseqr::ChromQual(file = file,chromlist = Chroms, windowSize = 1e+05, HighLimQuality = 15000, scalar = 1, ncol = 5, binwidth1 = 10, binwidth2 = 100, p1 = TRUE, p2 = TRUE, p3 = TRUE, p4 = TRUE, p5 = TRUE)
library(rMVP)
sample<-"ERR4835478"
pathtosample <- "/home/michael/Desktop/Alignment/plots/vcfnewsamplename.vcf"
out<- paste0("mvp.",sample,".vcf")
memo<-paste0(sample)
dffile<-paste0("mvp.",sample,".vcf.geno.map")
message("Making MVP data S1")
MVP.Data(fileVCF=pathtosample,
#filePhe="Phenotype.txt",
fileKin=FALSE,
filePC=FALSE,
out=out
)
message("Reading MVP Data S1")
df <- read.table(file = dffile, header=TRUE)
message("Making SNP Density Plots")
MVP.Report.Density(df[,c(1:3)], bin.size = 100000, col = c("blue", "yellow", "red"), memo = memo, file.type = "jpg", dpi=300)
https://www.aatbio.com/data-sets/amino-acid-reference-chart-table
#We can also use Qualimap for more analysis. I made an environment for this purpose.
#Select file drop down to New Analysis and finally BAMQC. Browse your directory for the sorted BAM file and >>>>> Start Analysis