demultiplexFASTQ: Demultiplex and tag fastq files using sample barcodes

In icetea: Integrating Cap Enrichment with Transcript Expression Analysis

Description

Demultiplex and tag fastq files using sample barcodes

Usage

demultiplexFASTQ(CSobject, outdir, max_mismatch = 0, ncores = 1)

## S4 method for signature 'CapSet'
demultiplexFASTQ(CSobject, outdir, max_mismatch = 0, ncores = 1)

Arguments

CSobject	CapSet object created using newCapSet function
outdir	character. path to output directory
max_mismatch	integer. maximum allowed mismatches in the sample barcode
ncores	integrer. No. of cores/threads to use

Value

de-multiplxed fastq files corresponding to each barcode. The files are written on disk with the corresponding sample names as specified in the CapSet object

Examples

# load a previously saved CapSet object
cs <- exampleCSobject()

# demultiplex allowing one mismatch in sample indexes
dir.create("demult_fastq")
cs <- demultiplexFASTQ(cs, outdir =  "demult_fastq", max_mismatch = 1)

icetea documentation built on Nov. 8, 2020, 6:57 p.m.