getUsedBarcodes: Create barcodes from the p5 and p7 index used for each...

In LihuaJulieZhu/GUIDEseq: GUIDE-seq and PEtag-seq analysis pipeline

Create barcodes from the p5 and p7 index used for each sequencing lane

Description

Create barcodes from the p5 and p7 index for assigning reads to each barcode

Usage

getUsedBarcodes(
  p5.index,
  p7.index,
  header = FALSE,
  reverse.p7 = TRUE,
  reverse.p5 = FALSE,
  outputFile
)

Arguments

p5.index	A text file with one p5 index sequence per line
p7.index	A text file with one p7 index sequence per line
header	Indicate whether there is a header in the p5.index and p7.index files. Default to FALSE
reverse.p7	Indicate whether to reverse p7 index, default to TRUE for standard GUIDE-seq experiments
reverse.p5	Indicate whether to reverse p5 index, default to FALSE for standard GUIDE-seq experiments
outputFile	Give a name to the output file where the generated barcodes are written

Value

DNAStringSet

Note

Create barcode file to be used to bin the reads sequenced in a pooled lane

Author(s)

Lihua Julie Zhu

Examples

    p7 <- system.file("extdata", "p7.index",
           package = "GUIDEseq")
    p5 <- system.file("extdata", "p5.index",
           package = "GUIDEseq")
    outputFile <- "usedBarcode"
    getUsedBarcodes(p5.index = p5, p7.index = p7, reverse.p7 = TRUE,
        reverse.p5 = FALSE, outputFile = outputFile)

LihuaJulieZhu/GUIDEseq documentation built on March 27, 2024, 9:42 p.m.