bsj_fastq_generate: bsj_fastq_generate

In Ularcirc: Shiny app for canonical and back splicing analysis (i.e. circular and mRNA analysis)

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")

Ularcirc documentation built on Nov. 8, 2020, 6:34 p.m.