score_guides

Add on-target activity and off-target specificity columns to a guide BED. On-target defaults to RuleSet3 (--tracr); add deep models with --cas9_scorer / --cas12a_scorer. Off-target specificity comes from each -i index (engine auto-detected).

crisprware score_guides -b chrIII_sequence_gRNA/chrIII_sequence_gRNA.bed \
  -i chrIII_sequence_crisprots/chrIII_sequence_crisprots --tracr Chen2013 --threads 8

#chr   start  stop   context                         strand sequence             RS3_score_Chen2013  specificity_chrIII_sequence_crisprots
chrIII 10569  10589  GCTGCCTACATGTACTTTTATTTGAGGGTC  +      CCTACATGTACTTTTATTTG -1.4272             1.0
chrIII 10590  10610  TTGAGGGTCCCCATGATCTTGAAGAGGAGA  +      GGGTCCCCATGATCTTGAAG -0.0695             1.0

One output column per scorer and per index. RuleSet3 is a z-score (centered at 0); specificity is 0-1 (1.0 = no off-targets).

Options you reach for

  • On-target: --tracr Hsu2013|Chen2013|both (RuleSet3); --cas9_scorer deepspcas9 deephf_wt_u6 ... or --cas12a_scorer deepcpf1 enpam_gb ... (--cas12a_variant <name> for the per-variant model). Multiple values allowed, one column each. See the on-target and off-target scoring pages for the menu.

  • Off-target: one or more -i indices (crispr-ots and/or guidescan2); --mismatches, --threshold (discard guides with an off-target within this many mismatches), and – guidescan2 only – --rna_bulges / --dna_bulges.

  • Speed / memory: --threads, --chunk_size (guides held in memory at once), --skip_rs3, --skip_gs2, --min_<scorer> (drop low scorers before the off-target pass).

  • Genome-wide Cas12a track: --ucscgb <dir> writes a UCSC Genome Browser Cas12a track instead of a scored BED (see the Cas12a UCSC tracks section).