AlleleProfileR.read.folders: Read folders for .fastq or .bam files

In abruyneel/AlleleProfileR: Genome editing strategy agnostic variant identification and profiling tool

Description

This function will scan the subfolders of files/input folder for .fastq.gz or .bam files, or the files/output folder for .bam files. To generate .bam files from .fastq files, the input folders should be scanned using the type = "fastq" parameter. Next, to conduct the analysis on .bam files that were generated in this step, use type = "bam". Please refer to the tutorial for more details.

Usage

AlleleProfileR.read.folders(type = "fastq")

Arguments

type	Input data type in the files/input folder, use either 'fastq' or 'bam'. If QC processing was conducted using AlleleProfileR, use fastq-clean.

Value

Sample table, listing the fastq or bam files for each sample.

Author(s)

Arne Bruyneel

abruyneel/AlleleProfileR documentation built on June 12, 2020, 2:47 p.m.