FastQFromSRR: Get Sequencing Data from the SRA

In npcooley/SynExtend: Tools for Working With Synteny Objects

Get Sequencing Data from the SRA

Description

Get sequencing data from the SRA.

Usage

FastQFromSRR(SRR,
             ARGS = list("--gzip" = NULL,
                         "--skip-technical" = NULL,
                         "--readids" = NULL,
                         "--read-filter" = "pass",
                         "--dumpbase" = NULL,
                         "--split-3" = NULL,
                         "--clip" = NULL),
             KEEPFILES = FALSE)

Arguments

SRR	A character vector of length 1 representing an SRA Run Accession, such as one that would be passed to the prefetch, fastq-dump, or fasterq-dump functions in the SRAToolkit.
ARGS	A list representing key and value sets used to construct the call to fastq-dump, multi-argument values are passed to paste directly and should be structured accordingly.
KEEPFILES	Logical indicating whether or not keep the downloaded fastq files outside of the R session. If TRUE, downloaded files will be moved to R's working directory with the default names assigned by fastq-dump. If FALSE - the default, they are removed and only the list of QualityScaledDNAStringSets returned by the function are retained.

Details

FastQFromSRR is a barebones wrapper for fastq-dump, it is set up for convenience purposes only and does not add any additional functionality. Requires a functioning installation of the SRAtoolkit.

Value

A list of QualityScaledDNAStringSets. The composition of this list will be determined by fastq-dump's splitting arguments.

Author(s)

Nicholas Cooley [e-mail]

Examples

x <- "ERR10466327"
y <- FastQFromSRR(SRR = x)

npcooley/SynExtend documentation built on Dec. 20, 2024, 4:03 p.m.