TraceQC: Creating an input object for TraceQC

In LiuzLab/TraceQC: Quality Control of CRISPR Lineage Tracing Seqence Data

Creating an input object for TraceQC

Description

Creating an input object for TraceQC

Usage

TraceQC(
  input_file,
  ref_file,
  fastqc_file = NULL,
  alignment_output_file = NULL,
  ncores = 4
)

Arguments

input_file	A FASTQ file path.
ref_file	A path of a reference sequence file.
fastqc_file	A path of a FASTQC file.
alignment_output_file	A path to store alignment output file. This will be ‘NULL’ if the output is temporally stored.
ncores	The number of cores for the parallel processing.

Value

It will return a list from ‘create_input_object_with_alignment’

Examples

library(TraceQC)
library(fastqcr)
input_file <- system.file("extdata", "test_data",
                          "fastq", "example_small.fastq.gz", package="TraceQC")
ref_file <- system.file("extdata", "test_data", "ref",
                        "ref.txt", package="TraceQC")
qc_dir <- fastqc.file(input_file)

input_qc_path <- get_qcpath(input_file, qc_dir)

obj <- TraceQC(input_file = input_file,
               ref_file = ref_file,
               fastqc_file = input_qc_path,
               ncores=1)

obj$refseq

LiuzLab/TraceQC documentation built on April 19, 2022, 1:29 p.m.