Run Perturb-seq direct-guide capture with a local agent

This route assigns a reviewed fixed read window to a finite direct-guide list. It is the same deterministic assignment contract used by CRISPR counting, with the narrower scientific boundary required for Perturb-seq guide-capture reads.

Exact inputs

  • targets: local TSV or CSV containing the known guide-barcode identifiers and sequences;

  • reads_dir: local directory containing only the intended guide-capture FASTQ or FASTQ.gz files;

  • output_dir: absent or empty local directory;

  • optional threads, max_reads, and max_start integers.

The target table must be known before assignment. DotMatch does not discover new guide sequences from the reads.

Copyable start

Create perturb-seq-request.json:

{
  "intent": "perturb-seq-guide-capture",
  "targets": "/absolute/path/direct-guides.tsv",
  "reads_dir": "/absolute/path/guide-capture-fastqs",
  "output_dir": "/absolute/path/dotmatch-perturb-seq-run",
  "threads": 4
}

dotmatch agent invoke prepare_assay --input perturb-seq-request.json

Pass the returned spec through inspect_assay, run_assay, review_assay, and—only when the reliability boundary permits it— handoff_assay. The JSON shapes are identical to the CRISPR agent route.

Outputs

  • inferred AssaySpec and inference evidence;

  • per-guide unique counts and optional per-read assignments;

  • separate ambiguous, unmatched, and invalid outcomes in QC and findings;

  • reliability, provenance, artifact hashes, resource use, and raw-data-free handoff records.

Evidence boundary

The GSE146194 reference evaluates a frozen 32-guide direct-capture rule on 48,000 held-out reads. DotMatch and matched independent per-read oracles have zero differences at k=0 and k=1 for that recorded dataset, target list, window, orientation, metric, and ambiguity rule.

This does not establish cell-barcode correction, UMI deduplication, guide-per-cell calls, expression quantification, indirect-capture designs, perturbation effects, or biological conclusions. Those steps and claims must remain outside the DotMatch handoff.