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

if (FALSE) {
# 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
)
}