createBarcodeFasta {GUIDEseq} | R Documentation

## Create barcode as fasta file format for building bowtie1 index

### 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)

[Package GUIDEseq version 1.10.0 Index]