demultiplexFastq {UMI4Cats} | R Documentation

## 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)

[Package UMI4Cats version 1.4.0 Index]