demultiplexFastq: Demultiplex FASTQ files using fastq-multx

In Pasquali-lab/UMI4Cats: UMI4Cats: Processing, analysis and visualization of UMI-4C chromatin contact data

Demultiplex FASTQ files using fastq-multx

Description

Demultiplex FASTQ files containng different bait information

Usage

demultiplexFastq(barcodes, fastq, out_path = "raw_fastq", numb_reads = 1e+11)

Arguments

barcodes	Dataframe with "name of sample" and "barcode" for every sample to demultiplex.
fastq	Fastq to demultiplex containing mate 1s. Different pairs should be named as "_R1" or "_R2". Allowed formats: _R1.fastq.gz, _R1.fq.gz, _R1.fastq or _R1.fq.
out_path	Path where to save the demultiplex output. Defaults to a path named raw_fastq in your working directory.
numb_reads	Number of lines from the FastQ file to load in each loop. If having memory size problems, change it to a smaller number. Default=10e10.

Value

Paired-end FastQ files demultiplexed in a compressed format. A log file with the statistics is also generated in out_path named barcode_umi4cats_demultiplexFastq_stats.txt.

Examples

## Not run: 
path <- downloadUMI4CexampleData(use_sample = TRUE)
fastq <- file.path(path, "CIITA", "fastq", "sub_ctrl_hi19_CIITA_R1.fastq.gz")
barcodes <- data.frame(
    sample = c("CIITA"),
    barcode = c("GGACAAGCTCCCTGCAACTCA")
)

demultiplexFastq(
    barcodes = barcodes,
    fastq = fastq,
    out_path = path
)

## End(Not run)

Pasquali-lab/UMI4Cats documentation built on Nov. 3, 2024, 3:10 p.m.