---
title: "CRISPR on-target activity (Rule Set 3)"
method: POST
path: "/crispr_ontarget"
tags: ["CRISPR"]
---

# CRISPR on-target activity (Rule Set 3)

`POST /crispr_ontarget`

## Request

- Base URL: `https://seqbench.com/api/v1`
- URL: `https://seqbench.com/api/v1/crispr_ontarget`
- Auth: none required

Score SpCas9 guides for on-target activity with Rule Set 3 (DeWeirdt et al., Nat Commun 2022) — the current successor to the Doench 2014 and CRISPRscan scores crispr_grna_design reports. Give a target sequence to find and score every NGG guide in it — on both strands unless `searchReverseStrand` says otherwise — or give 30-mer contexts directly. The tracrRNA MATTERS and is not cosmetic: Rule Set 3 models it as a feature, and the paper measures its accuracy dropping when the wrong one is specified. Returns a z-scored activity, which ranks guides against each other; it is not a percentage and not a probability of editing.

## Request body

- object
  - `sequence` string: Target DNA to find NGG guides in. Give this OR `contexts`.
  - `contexts` string[]: 30-mer contexts to score directly: 4 nt upstream + 20 nt spacer + PAM + 3 nt downstream. Give this OR `sequence`.
  - `searchReverseStrand` boolean: Also scan the reverse strand for guides. Applies to `sequence` only; a 30-mer in `contexts` is already written on its own guide's strand.
  - `tracr` 'Hsu2013' | 'Chen2013': Which tracrRNA the guides will be paired with. Hsu2013 is the one in lentiCRISPRv2 and most published libraries; Chen2013 is the sgRNA(F+E) scaffold used by the Sanger/Yusa libraries. If you use the DeWeirdt (2020) tracrRNA, the paper reports Chen2013 as the better proxy — there is no DeWeirdt option in the model itself.

## Response `200`

Tool ran successfully.

- SuccessResponse: Standard success envelope returned by every single-tool call.
  - `ok` unknown, required
  - `tool` string, required: The tool slug that ran.
  - `result` object, required: Tool-specific output object. Its shape depends on the tool — call `GET /{tool}` or see the docs for each tool's fields.
  - `gate` GateResult
    - `pass` boolean, required: True if and only if every hard check passed.
    - `checks` GateCheck[], required
      - `id` string, required
      - `label` string, required
      - `severity` 'hard' | 'soft', required
      - `pass` boolean, required
      - `message` string, required
      - `value` number
      - `threshold` string
    - `notChecked` string[], required: Honest list of what this gate does NOT verify.
  - `provenance` Provenance, required
    - `apiVersion` string, required
    - `tool` union, required: Tool slug, or an array of slugs (one per step) for a workflow.
      - string
      - string[]
    - `generatedAt` string, date-time, required: ISO 8601 timestamp of when the result was generated.

## Other responses

- `400`: Invalid argument or the tool could not run.
- `404`: Unknown tool.
- `429`: Rate limited (metered tools only). Body carries code `rate_limited` and retryable `true`; honor the Retry-After header.
- `503`: A metered tool is momentarily at capacity. The identical request should succeed after Retry-After; body carries code `upstream_unavailable`.

---

[API](https://skmtc.dev/seqbench/apis/seqbench-api.md) · [All operations](https://skmtc.dev/seqbench/apis/seqbench-api/llms.txt) · [OpenAPI document](https://skmtc.dev/seqbench/apis/seqbench-api/revisions/132575216865?raw)