uniqueBar: Tool function to obtain unique barcode sequences from a...

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

Description

This a function for removing the duplicated barcodes in the library file that will be used for the bcSeq alignment.

Usage

uniqueBar(inputFile,outputFile)

Arguments

inputFile	(string) filename for the library sequences, needs to be a fasta or fastq file.
outputFile	(string) output filename.

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 <- 20
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 = '')
}
Barcodes <- rbind(Barcodes, Barcodes)
write(Barcodes, lFName)

outFile  <- "./libFile_unique.fasta"
uniqueBar(lFName, outFile)

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