seeFastq {systemPipeR} | R Documentation

## Quality reports for FASTQ files

### Description

The following `seeFastq` and `seeFastqPlot` functions generate and plot a series of useful quality statistics for a set of FASTQ files including per cycle quality box plots, base proportions, base-level quality trends, relative k-mer diversity, length and occurrence distribution of reads, number of reads above quality cutoffs and mean quality distribution. The functions allow processing of reads with variable length, but most plots are only meaningful if the read positions in the FASTQ file are aligned with the sequencing cycles. For instance, constant length clipping of the reads on either end or variable length clipping on the 3' end maintains this relationship, while variable length clipping on the 5' end without reversing the reads erases it.

The function seeFastq computes the summary stats and stores them in a relatively small list object that can be saved to disk with `save()` and reloaded with `load()` for later plotting. The argument 'klength' specifies the k-mer length and 'batchsize' the number of reads to random sample from each fastq file.

### Usage

    seeFastq(fastq, batchsize, klength = 8)

    seeFastqPlot(fqlist, arrange = c(1, 2, 3, 4, 5, 8, 6, 7), ...)

### Arguments

`fastq` | Named character vector containing paths to FASTQ file in the data fields and sample labels in the name slots.
`batchsize` | Number of reads to random sample from each FASTQ file that will be considered in the QC analysis. Smaller numbers reduce the memory footprint and compute time.
`klength` | Specifies the k-mer length in the plot for the relative k-mer diversity.
`fqlist` | `list` object returned by `seeFastq()`.
`arrange` | Integer vector from 1 to 7 specifying the row order of the QC plot. Dropping numbers eliminates the corresponding plots.
`...` | Additional plotting arguments to pass on to `seeFastqPlot()`.

### Value

The function `seeFastq` returns the summary stats in a `list` containing all information required for the quality plots. The function `seeFastqPlot` plots the information generated by `seeFastq` using `ggplot2`.

### Author(s)

Thomas Girke

### Examples

    ## Not run:
    targets <- system.file("extdata", "targets.txt", package="systemPipeR")
    dir_path <- system.file("extdata/cwl/hisat2/hisat2-se", package="systemPipeR")
    args <- loadWorkflow(targets=targets, wf_file="hisat2-mapping-se.cwl",
                      input_file="hisat2-mapping-se.yml", dir_path=dir_path)
    args <- renderWF(args, inputvars=c(FileName="_FASTQ_PATH1_", SampleName="_SampleName_"))
    fqlist <- seeFastq(fastq=infile1(args), batchsize=10000, klength=8)
    pdf("fastqReport.pdf", height=18, width=4*length(fastq))
    seeFastqPlot(fqlist)
    dev.off()

    ## End(Not run)

[Package systemPipeR version 1.21.6 Index]