getSubsetReads: Subsetting fastq data

In tgirke/systemPipeRdata: systemPipeRdata: Workflow templates and sample data

Subsetting fastq data

Description

Returns subsets of fastq files data based on specific mapping regions or list of genes or GRanges object.

Usage

getSubsetReads(args,
  geneList = NULL,
  gr = NULL,
  MappingRegion = 1:1e+05,
  sample_range = 90000:1e+05,
  truncate_refs = TRUE,
  id_read_number = TRUE,
  annotation = "data/tair10.gff",
  reference = "data/tair10.fasta",
  annot_outname = "tair10_sub.gff",
  ref_outname = "tair10_sub.fasta",
  outdir = "data/subset/",
  silent = FALSE
)

Arguments

args	object of class SYSargs2.
geneList	selected genes list to retrieve the reads from the fastq file.
gr	an object containing genomic ranges to retrieve the reads from the fastq file.
MappingRegion	integers ranges of start and end of chromosome position to retrieve the reads from the fastq file.
sample_range	random range to subsetted the fastq file.
truncate_refs	logical. If TRUE it will generate reference genome and annotation subset file.
id_read_number	if fastq file contains sequence name with read number (⁠$ri⁠ - ⁠--defline-seq '@$sn[_$rn]/$ri'⁠).
annotation	path to annotation file.
reference	path to reference genome.
annot_outname	character name of the annotation output file.
ref_outname	character name of the reference genome output file.
outdir	path to output directory.
silent	if set to TRUE, all messages returned by the function will be suppressed.

Value

Workflow directory containing sample data and parameter files along with the following subdirectories:

param/	stores parameter files
data/	stores input data
results/	stores output results

For more details, please consult the Overview Vignette (HTML) of the systemPipeR package (http://bioconductor.org/packages/systemPipeR).

Author(s)

Thomas Girke, Shiyuan Guo and Daniela Cassol

Examples

## Not run: 
getSubsetReads(args, MappingRegion = 1:900, sample_range = 800:900, outdir = "data/subset/", silent = FALSE)
getSubsetReads(args, MappingRegion = 1:900, sample_range = NULL, outdir = "data/subset/", silent = FALSE)

## End(Not run)

tgirke/systemPipeRdata documentation built on Oct. 19, 2023, 9:20 p.m.