oligo.design.OffTarget¶

class oligo.design.OffTarget(genome, fa, config_path, blat=False)[source]¶

Designs oligos adjacent to potential CRISPR off-target sites

Parameters:

Attributes:

blatbool: Check off-target binding using BLAT instead of STAR (not recommended for large designs), default = False
fastastr: Name of fasta file for oligo sequences, default = oligo_seqs.fa
oligo_seqsdict: Contains all oligo sequences after generating oligos

Methods

`align_to_genome`([s_idx])	Aligns oligos to the genome using BLAT or STAR
`calculate_density`([sam, blat_file])	Calculates the repeat scores and off-target binding for each oligo based on their scores from RepeatMasker and STAR/BLAT.
`detect_repeats`()	Detects repeat sequences in oligos, using RepeatMasker
`extract_repeats`()	Extracts information of repeat content from RepeatMasker output file for every oligo
`gen_oligos`(bed[, oligo, step, max_dist])	Designs oligos adjacent to user-supplied coordinates for potential CRISPR off-target cleavage sites
`write_fasta`()	Writes oligo_seqs attribute to fasta file
`write_oligo_info`()	Writes oligo stats to oligo_info.txt

gen_oligos(bed, oligo=70, step=10, max_dist=200)[source]¶

Designs oligos adjacent to user-supplied coordinates for potential CRISPR off-target cleavage sites

Parameters:

bedstr: Path to tab-delimited bed file containing a list of coordinates for viewpoints in the capture experiment; must be in the format ‘chr’\t’start’\t’stop’\t’name’\n
oligoint, optional: The length of the oligo to design (bp), default=70
stepint, optional: The step size, or how close adjacent oligos should be, default=10; for end-to-end oligos, set step to equal oligo
max_distint, optional: The maximum distance away from the off-target site to design oligos to, default = 200

Returns:

oligo