alignSTAR: STAR alignment

In SchwartzLab/brainSTORM: brainSTORM. A package to process STORM-seq based data

STAR alignment

Description

Wrapper to perform alignment of sequencing reads to a reference genome using STAR (Dobin) and sorting and indexing using Samtools.

Usage

alignSTAR(
  read1Files,
  STARgenomeDir,
  pairedEnd = TRUE,
  zipped = TRUE,
  nCores = 4,
  alignEndsType = "Local",
  alignIntronMax = 0,
  outFilterMultimapNmax = 10,
  outDir,
  otherSTARparams = "",
  dry = FALSE
)

Arguments

read1Files	character. Path to R1 FASTQ files
STARgenomeDir	character. Path to STAR genome to map to
pairedEnd	logical. Indicating if to expect a Read2 FASTQ file File will be automatically looked for but both need to include "_R1", and "_R2" in their respective file names.
zipped	logical. TRUE as default for zipped FASTQ files, will be read with zcat. If set to FALSE FASTQ files will be read with cat, as not zipped.
nCores	numeric. Number of cores used for alignment and sorting processes.
alignEndsType	character. type of read ends alignment (See STAR manual for more info)
alignIntronMax	numeric. maximum intron size, if 0, max intron size will be determined by default as (2ˆwinBinNbits)*winAnchorDistNbins (See STAR manual for more info)
outFilterMultimapNmax	numeric. Threshold for which a read will have multiple mappings. Default is 10. For unique alignment change the value to 1.
outDir	character. Path to output directory
otherSTARparams	character. Additional parameters not covered by the arguments of this function can be added here, separated by spaces.
dry	logical. If set to TRUE the alignment is not performed, only output are the paths to expected output files.

SchwartzLab/brainSTORM documentation built on May 14, 2022, 5:14 p.m.