RunMiXCRseqAlignment: RNAseqAlignment

In elmerfer/RMiXCR: An easy wrapper for MiXCR software

RNAseqAlignment

Description

This function aligns raw sequencing reads to reference V, D, J and C genes of T- and B- cell receptors.

Usage

RunMiXCRseqAlignment(sbj, species = c("hsa","mmu","rat"), extendedAlignments=FALSE, nThreads = 4L)

Arguments

sbj	full path to the subject.R1.fastq sample file. The paired read should be named subject.R2.fastq
species	any of "hsa","mmu", "rat" (human - mouse, rat)
extendedAlignments	(logical, default TRUE) if TCR extension alignment should be performed (in case of incomplete TCR alignments)
nThreads	(integer) number of cores (default 4, since it is suggested as the optimum value)

Value

It will generate file named "subject.R1.fastq.alignments.vdjca" the full path to this file is returned to be used as input to RunMiXCRseqClones

Examples

/dontrun{
      subj.file <- "/home/.../subject.R1.fastq"
      out.vdja.file <- RunMiXCR(sbj = subj.file)
      print(out.vdja.file)
}

elmerfer/RMiXCR documentation built on May 27, 2023, 5:08 a.m.