bsj_fastq_generate {Ularcirc} | R Documentation

## bsj_fastq_generate

### Description

Takes a circRNA predicted sequence and generates synthetic short sequence reads

### Usage

    bsj_fastq_generate(circRNA_Sequence, fragmentLength = 300,
      readLength = 100, variations = 4, headerID = "")

### Arguments

`circRNA_Sequence` | : Linear sequence of a circRNA. i.e. the backspice junction is the first and last base of this sequence
`fragmentLength` | : Is the length the library fragment
`readLength` | : The sequence read length
`variations` | : Number of sequences returned for each read type. Note each sequence variation will start at a unique location (where possible)
`headerID` | : Character identifier that will be incorporated into sequence header

### Value

Returns a list of two DNAstring sets labelled "read1" and "read2" which correspond to forward and reverse read pairs.

### Examples

    library('Ularcirc')

    # Generate a 500nt sequence containing A" and which is flanked with GG and CC.
    circRNA_Sequence <- paste(rep('A',500),collapse='')
    circRNA_Sequence <- paste('GG',circRNA_Sequence, 'CC', sep='')
    # The GG and CC ends of sequence represent ends of linear exons that are circularised.
    # Therefore the backsplice junction (BSJ) is GGCC.
    # Generate reads that alternate over this BSJ

    fastqReads <- bsj_fastq_generate(circRNA_Sequence, fragmentLength=300, readLength=100,
                   variations = 4,   # Four type I , II, III, and IV reads generated
                   headerID='circRNA_example')  # Identifier incorporated in name of each sequence
    # The following will indicate 12 sequences are present in each list entry
    length(fastqReads$read1)
    length(fastqReads$read2)

    # Can create fastq file as follows
    Biostrings::writeXStringSet( fastqReads$read1,"circRNA_Sample_R1.fastq.gz",
                                  compress = TRUE, format="fastq")
    Biostrings::writeXStringSet( fastqReads$read2,"circRNA_Sample_R2.fastq.gz",
                                  compress = TRUE, format="fastq")

[Package Ularcirc version 1.4.0 Index]