trimRead {bcSeq} | R Documentation

## Tool function to trim adaptor for read sequences.

### Description

This a function for triming reads with adaptor. The sequencing within [start, end] will be written to the output file.

### Usage

    trimRead(inputFile,outputFile, start, end)

### Arguments

`inputFile` | (string) filename for the library sequences, needs to be a fasta or fastq file.
`outputFile` | (string) output filename.
`start` | (integer) starting position.
`end` | (integer) ending position.

### Value

`default` | No objects are returned to R

### Examples

    #### Generate barcodes
    lFName    <- "./libFile.fasta"
    bases     <- c(rep('A', 4), rep('C',4), rep('G',4), rep('T',4))
    numOfBars <- 40
    Barcodes  <- rep(NA, numOfBars*2)
    for (i in 1:numOfBars){
        Barcodes[2*i-1] <- paste0(">barcode_ID: ", i)
        Barcodes[2*i]   <- paste(sample(bases, length(bases)), collapse = '')
    }
    write(Barcodes, lFName)

    #### Generate reads and phred score
    rFName     <- "./readFile.fastq"
    numOfReads <- 800
    Reads      <- rep(NA, numOfReads*4)
    for (i in 1:numOfReads){
        Reads[4*i-3] <- paste0("@read_ID_",i)
        Reads[4*i-2] <- Barcodes[2*sample(1:numOfBars,1,
            replace=TRUE, prob=seq(1:numOfBars))]
        Reads[4*i-1] <- "+"
        Reads[4*i]   <- paste(rawToChar(as.raw(
            33+sample(20:30, length(bases),replace=TRUE))),
            collapse='')
    }
    write(Reads, rFName)

    #### perform alignment
    outFile  <- "./readFile_trimReaded.fastq"
    trimRead(rFName, outFile, 5,15)

[Package bcSeq version 1.12.0 Index]