createBasemasks: Function to create basemasks for basecalling from Illumina...

In ThomasCarroll/basecallQC: Working with Illumina Basecalling and Demultiplexing input and output files

Description

Parses the Illumina sample sheet for versions >= 2.1.7 and creates basemasks.

Usage

createBasemasks(cleanedSampleSheet, param)

Arguments

cleanedSampleSheet	Data.frame of cleaned samplesheet for Illumina basecalling using bcl2Fastq versions >= 2.1.7 (see vignette for more details)
param	A BCL2FastQparams object

Value

A data.frame containing basecall masks per lane for reads and indexes as well as per lane complete basemasks.

Author(s)

Thomas Carroll and Marian Dore

Examples

fileLocations <- system.file("extdata",package="basecallQC")
runXML <- dir(fileLocations,pattern="runParameters.xml",full.names=TRUE)
config <- dir(fileLocations,pattern="config.ini",full.names=TRUE)
sampleSheet <- dir(fileLocations,pattern="*\\.csv",full.names=TRUE)
bcl2fastqparams <- BCL2FastQparams(runXML,config,runDir=getwd(),verbose=FALSE)

cleanedSampleSheet <- validateBCLSheet(sampleSheet,param=bcl2fastqparams)
basemasks <- createBasemasks(cleanedSampleSheet,param=bcl2fastqparams)

ThomasCarroll/basecallQC documentation built on May 9, 2019, 4:45 p.m.