Multiple and parallel sequence quality assessment

Introduction to Bioconductor in R

Paula Andrea Martinez, PhD.

Data Scientist

Rqc

library(Rqc)

Uses Bioconductor packages that you have already used:
- Biostrings, IRanges, methods, S4vectors
New packages to discover in the following Bioconductor courses:
- Rsamtools, GenomicAlignments, GenomicFiles, BiocParallel
CRAN packages:
- Knitr, dplyr, markdown, ggplot2, digest, shiny, and Rcpp

rqcQA

library(Rqc)
files <- # get the full path of the files you want to assess
qaRqc <- rqcQA(files) 

# exploring qaRqc
class(qaRqc) # "list"
names(qaRqc) # name of the input files

# for each file
qaRqc[1]
# the class of the results is RqcResultSet

rqcQA arguments

library(Rqc)

# get the path of the files you want to assess
files <- "data/seq1.fq" "data/seq2.fq" "data/seq3.fq" "data/se4.fq"

qaRqc <- rqcQA(files, workers = 4)

# sample of sequences
set.seed(1111)

qaRqc_sample <- rqcQA(files, workers = 4, sample = TRUE, n = 500))

# paired-end files
pfiles <- "data/seq_11.fq" "data/seq1_2.fq" "data/seq2_1.fq" "data/seq2_2.fq"

qaRqc_paired <- rqcQA(pfiles, workers = 4, pair = c(1, 1, 2, 2)))

rqcReport and rqcResultSet

# create a report
reportFile <- rqcReport(qaRqc, templateFile = "myReport.Rmd")

browseURL(reportFile)

#The class of qaRqc is rqcResultSet
methods(class = "RqcResultSet")

perFileInformation

qaRqc <- rqcQA(files, workers = 4)) 
perFileInformation(qaRqc)

filename          pair format  group  reads total.reads   path 
SRR7760274.fastq  1    FASTQ    None  1e+06     2404795 ./data
SRR7760275.fastq  2    FASTQ    None  1e+06     1508139 ./data
SRR7760276.fastq  3    FASTQ    None  1e+06     1950463 ./data
SRR7760277.fastq  4    FASTQ    None  1e+06     2629588 ./data

Plot functions

rqc Plot functions	rqc Plot functions
`rqcCycleAverageQualityPcaPlot()`	`rqcGroupCycleAverageQualityPlot()`
`rqcCycleAverageQualityPlot()`	`rqcReadQualityBoxPlot()`
`rqcCycleBaseCallsLinePlot()`	`rqcReadQualityPlot()`
`rqcCycleBaseCallsPlot()`	`rqcReadWidthPlot()`
`rqcCycleGCPlot()`	`rqcReadFrequencyPlot()`
`rqcCycleQualityBoxPlot()`	`rqcCycleQualityPlot()`

cycle-basecall-lineplots

KEEP CALM

You are ready!

Introduction to Bioconductor in R