createBarcodeFasta: Create barcode as fasta file format for building bowtie1...

In GUIDEseq: GUIDE-seq analysis pipeline

Description

Create barcode as fasta file format for building bowtie1 index to assign reads to each library with different barcodes. The bowtie1 index has been built for the standard GUIDE-seq protocol using the standard p5 and p7 index. It can be downloaded at http://mccb.umassmed.edu/GUIDE-seq/barcode.bowtie1.index.tar.gz

Usage

createBarcodeFasta(p5.index, p7.index, reverse.p7 = TRUE, 
    reverse.p5 = FALSE, header = FALSE, outputFile = "barcodes.fa")

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. This file can be used to build bowtie1 index for binning reads.

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 <- "barcodes.fa" 
    createBarcodeFasta(p5.index = p5, p7.index = p7, reverse.p7 = TRUE,
        reverse.p5 = FALSE, outputFile = outputFile)

GUIDEseq documentation built on Nov. 8, 2020, 5:27 p.m.