demultiplexFastq {UMI4Cats} | R Documentation |
Demultiplex FASTQ files containng different bait information
demultiplexFastq(barcodes, fastq, out_path = "raw_fastq", numb_reads = 1e+11)
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 |
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. |
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.
## 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)