catfastq {Rfastp} | R Documentation |
concatenate multiple fastq files into a single file.
catfastq(output, inputFiles, append = FALSE, paired = FALSE, shuffled = FALSE)
output |
output file name [string] |
inputFiles |
a vector of input file names [vector] |
append |
a logical indicating append the files to a file already exists. |
paired |
a logical indicating split the input files into two halves. the first half merged into read1, the second half merged into read2. |
shuffled |
a logical indicating split the input file list into two halves. The R1/R2 files are inteleaved in the inputFiles vector. |
no returns.
Wei Wang
pe001_read1 <- system.file("extdata","splited_001_R1.fastq.gz", package="Rfastp") pe002_read1 <- system.file("extdata","splited_002_R1.fastq.gz", package="Rfastp") pe003_read1 <- system.file("extdata","splited_003_R1.fastq.gz", package="Rfastp") pe004_read1 <- system.file("extdata","splited_004_R1.fastq.gz", package="Rfastp") pe001_read2 <- system.file("extdata","splited_001_R2.fastq.gz", package="Rfastp") pe002_read2 <- system.file("extdata","splited_002_R2.fastq.gz", package="Rfastp") pe003_read2 <- system.file("extdata","splited_003_R2.fastq.gz", package="Rfastp") pe004_read2 <- system.file("extdata","splited_004_R2.fastq.gz", package="Rfastp") allR1 <- c(pe001_read1, pe002_read1, pe003_read1, pe004_read1) allR2 <- c(pe001_read2, pe002_read2, pe003_read2, pe004_read2) allreads <- c(allR1, allR2) allreads_shuffled <- c(pe001_read1, pe001_read2, pe002_read1, pe002_read2, pe003_read1, pe003_read2, pe004_read1, pe004_read2) outputPrefix <- tempfile(tmpdir = tempdir()) # a normal concatenation for single-end libraries. catfastq(output = paste0(outputPrefix, "_R1.fastq.gz"), inputFiles = allR1) # a normal concatenation for paired-end libraries. catfastq(output = paste0(outputPrefix, "merged_paired"), inputFiles = allreads, paired=TRUE) # Append to exist files (paired-end) catfastq(output=paste0(outputPrefix,"append_paired"), inputFiles=allreads, append=TRUE, paired=TRUE) # Input paired-end files are shuffled. catfastq(output=paste0(outputPrefix,"_shuffled_paired"), inputFiles=allreads_shuffled, paired=TRUE, shuffled=TRUE)