trimRead {bcSeq} | R Documentation |
This a function for triming reads with adaptor. The sequencing within [start, end] will be written to the output file.
trimRead(inputFile,outputFile, start, end)
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. |
default |
No objects are returned to R |
#### 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)