bsj_fastq_generate {Ularcirc} | R Documentation |
Takes a circRNA predicted sequence and generates synthetic short sequence reads
bsj_fastq_generate(circRNA_Sequence, fragmentLength = 300, readLength = 100, variations = 4, headerID = "")
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) |
headID |
: Character identifier that will be incorporated into sequence header |
Returns a list of two DNAstring sets labelled "read1" and "read2" which correspond to forward and reverse read pairs.
library('Ularcirc') # Obtain a circRNA sequence circRNA_Sequence <- "GGAAGAGGAAGAACGTCTGAGAAATAAAATTCGAGCTGATCATGAGAAGGCCTTGGAAGAAGCAAAAGAAAAATTAAGAAAGTCAAGAGAGGAAATTCGAGCAGAAATTCAGACAGAGAAAAATAAGGTAGTCCAAGAAATGAAGATAAAAGAGAACAAGCCACTGCCACCAGTCCCTATTCCCAACCTTGTAGGAATACGTGGTGGAGACCCAGAAGATAATGACATAAGAGAGAAAAGGGAAAAAATTAAAGAGATGATGAAACATGCTTGGGATAACTATAGGACATATGGGTGGGGACATAATGAACTCAGACCTATTGCAAGGAAAGGACACTCCCCTAACATATTTGGAAGTTCACAAATGGGTGCTACCATAGTAGATGCTTTGGATACCCTTTATATCATGGGACTTCATGATGAATTCCTAGATGGGCAAAGATGGATTGAAGACAACCTTGATTTCAGTGTGAATTCAGAGGTGTCTGTGTTTGAAGTCAACATTCGATTTATTGGAGGCCTACTTGCAGCATATTACCTATCAGGAGAGGAG" 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")