CRISPRware

Getting started

  • Installation
    • 1. Python environment
    • 2. The crispr-ots scanner
      • Prebuilt binary
      • Build it yourself
    • Verify
    • Docker
    • Memory
  • Quickstart
    • 1. Gene models
    • 2. Off-target index
    • 3. Generate guides
    • 4. Score guides
    • 5. Rank guides
  • Tutorials

Modules

  • Modules
    • preprocess_annotation
      • Options you reach for
    • index_genome
      • Options you reach for
    • generate_guides
      • Options you reach for
      • PAM geometry
    • score_guides
      • Options you reach for
    • rank_guides
      • Options you reach for
  • NGS-guided design
    • RNA-seq: keep expressed isoforms
    • Ribo-seq: target translated ORFs

Scoring

  • Scoring methods
    • On-target scoring
      • RuleSet3
      • DeepSpCas9
      • DeepHF
      • DeepCpf1
      • enPAM+GB
      • enseq-DeepCpf1
      • seq-DeepCpf1variants
    • Off-target scoring
      • crispr-ots
      • Guidescan2
      • Controls (in score_guides)
    • crisprScore integration (optional, R)

Cas12a UCSC tracks

  • The UCSC Cas12a track pipeline
    • Overview
      • Cas12a specifics
      • The off-target asymmetry that drives the index
      • References
    • Setup
      • Environment variables
      • The CLI
      • Input genome
    • Index and guides
      • 1. Off-target index (PAM TTTN)
      • 2. Enumerate TTTV protospacers
    • Score and assemble the track
      • Flags, grouped
      • What --ucscgb_chunk_max does
      • Worked example (hg38, 7x A5500)
    • Outputs
      • What you get
      • Reading a details record
  • Reading the track
    • The bigBed columns
      • The eight score columns read percentile (raw)
      • score and color
    • Off-target records
      • Coordinate geometry
      • _offset = 0 and uniqueness

Reference

  • Command reference
    • preprocess_annotation
    • index_genome
    • generate_guides
    • score_guides
    • rank_guides
  • References
CRISPRware
  • Search

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