MiTCR: Run MiTCR on each fastQ file

In RGLab/RNASeqPipelineR: Construct Standardized pipelines for processing RNASeq data

Description

Run the MiTCR tool on each fastQ file

Usage

MiTCR(gene = "TRB", species = NULL, ec = 2, pset = "flex",
  ncores = 1, output_format = "text", paired = FALSE)

Arguments

gene	character c("TRB","TRA")
species	character c("hs","mm")
ec	integer, c(0,1,2)
pset	character c("flex")
ncores	integer number of cores for running in parallel
output_format	character either "txt" or "cls". cls files can be viewed in the MiTCR viewer. Txt files can be parsed and used to annotate libraries.
paired	logical specify whether data is paired (in which case the fastq files in PEAR directory are used). Defaults to FALSE.

Details

Runs MiTCR on each fastQ file.

RGLab/RNASeqPipelineR documentation built on Jan. 19, 2020, 12:31 a.m.