Index

Symbols

--bed command line option, [1] --blat command line option, [1], [2] --chr command line option --contig command line option --enzyme command line option, [1] --fasta command line option, [1], [2] --genome command line option, [1], [2] --help command line option, [1], [2] --max_dist command line option --oligo command line option, [1], [2] --region command line option --star_index command line option, [1], [2]

--step_size command line option, [1] -b command line option, [1] -c command line option -e command line option, [1] -f command line option, [1], [2] -g command line option, [1], [2] -h command line option, [1], [2] -m command line option -o command line option, [1], [2] -r command line option -s command line option, [1], [2] -t command line option, [1]

_

_create_attr() (oligo.tools.Tools method) _get_gc() (oligo.tools.Tools method)

_populate_oligo_stats() (oligo.tools.Tools method) _run_command() (oligo.tools.Tools method) _sort_file() (oligo.tools.Tools method)

A

align_to_genome() (oligo.tools.Tools method)

C

calculate_density() (oligo.tools.Tools method) Capture (class in oligo.design) command line option --bed, [1] --blat, [1], [2] --chr --contig --enzyme, [1] --fasta, [1], [2] --genome, [1], [2] --help, [1], [2] --max_dist --oligo, [1], [2] --region --star_index, [1], [2] --step_size, [1] -b, [1] -c -e, [1] -f, [1], [2] -g, [1], [2] -h, [1], [2] -m -o, [1], [2] -r -s, [1], [2] -t, [1]

D

detect_repeats() (oligo.tools.Tools method)

E

extract_repeats() (oligo.tools.Tools method)

G

gen_oligos() (oligo.design.Capture method) (oligo.design.OffTarget method)

gen_oligos_capture() (oligo.design.Tiled method) gen_oligos_contig() (oligo.design.Tiled method)

O

OffTarget (class in oligo.design)

T

Tiled (class in oligo.design)

Tools (class in oligo.tools)

W

write_fasta() (oligo.tools.Tools method)

write_oligo_info() (oligo.tools.Tools method)