trimRead: Tool function to trim adaptor for read sequences.

In bcSeq: Fast Sequence Mapping in High-Throughput shRNA and CRISPR Screens

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)

Example output

bcSeq documentation built on Nov. 8, 2020, 8:03 p.m.