SplitSRA: Split SRA to fastq Files and Format to 10x Standard Style.

In scfetch: Access and Format Single-Cell RNA-Seq Datasets from Public Resources

Split SRA to fastq Files and Format to 10x Standard Style.

Description

Split SRA to fastq Files and Format to 10x Standard Style.

Usage

SplitSRA(
  sra.folder = NULL,
  sra.path = NULL,
  fastq.type = c("10x", "other"),
  split.cmd.path = NULL,
  sratools.path = NULL,
  split.cmd.paras = NULL,
  split.cmd.threads = NULL,
  format.10x = TRUE,
  remove.raw = FALSE
)

Arguments

sra.folder	Folder contains all sras, obtained from DownloadSRA. Default: NULL.
sra.path	Paths of sras. sra.folder and sra.path cannot be both NULL. Default: NULL.
fastq.type	The source of fastq files, choose from 10x (use --split-files to split sra) or other (use --split-3 to split sra). Default: 10x.
split.cmd.path	The full command path used to split, can be path to parallel-fastq-dump, fasterq-dump and fastq-dump. Default: NULL (conduct automatic detection).
sratools.path	Path to sratoolkit bin. When split.cmd.path is path to parallel-fastq-dump, it requires sratoolkit. Default: NULL (conduct automatic detection).
split.cmd.paras	Parameters for split.cmd.path. Default: NULL.
split.cmd.threads	Threads, used when split.cmd.path is path to parallel-fastq-dump or fasterq-dump. Default: NULL (1).
format.10x	Logical value, whether to format split fastqs to 10x standard format. Default: TRUE.
remove.raw	Logical value, whether to remove old split fastqs (unformatted), used when format.10x is TRUE. Default: FALSE.

Value

NULL or paths of failed sras.

Examples

## Not run: 
# need users to provide the prefetch.path, sra.folder, split.cmd.path, sratools.path and out.folder
GSE186003.runs <- ExtractRun(acce = "GSE186003", platform = "GPL24247")
GSE186003.down <- DownloadSRA(
  gsm.df = GSE186003.runs, prefetch.path = "/path/to/prefetch",
  out.folder = "/path/to/output"
)
GSE186003.split <- SplitSRA(
  sra.folder = "/path/to/output",
  split.cmd.path = "/path/to/parallel-fastq-dump",
  sratools.path = "/path/to/sra/bin", fastq.type = "10x",
  split.cmd.threads = 4
)

## End(Not run)

scfetch documentation built on Nov. 22, 2023, 1:09 a.m.