crispr_quantify_edits
Read-only
Quantify a CRISPR edit from a pair of Sanger traces — how much of the population was edited, what the indel spectrum looks like, and how well the model fits. Synthego ICE: the CONTROL trace gives the unedited sequence, the EDITED trace is decomposed into a mixture of proposed indels around each guide's cut, and the abundances are fitted. Answers the question a screen cannot: not whether a guide is good, but what it actually did to these cells.
Input Schema
| Name | Required | Description | Default |
|---|---|---|---|
| donor | No | optional HDR donor / ssODN. Given one, ICE also proposes the recombination outcome and reports an HDR percentage; left empty there is no HDR arm rather than a zero. | |
| _files | No | The project: record references shaped like _subject. Their records become library documents a tool names in sequences/parts/document; a trace or alignment is found by file name. | |
| edited | Yes | the EDITED trace, by file name or id. | |
| guides | Yes | the guide spacers, RNA accepted. Each is located in the CONTROL on either strand, so the cut sites come from the data rather than from a coordinate you supply. | |
| control | Yes | the UNEDITED trace, by file name or id — it supplies the reference the edited read is decomposed against. | |
| _subject | No | The record to act on: exactly one of sequence, accession (+source), sample (an id from list_samples) or file ({name, text} or {name, base64}); record_index picks one record of several. | |
| base_editing | No | also fit every single-base change on the PAM-distal side of each cut, for a base editor. Left false, the scores stay comparable with published ICE numbers, which the extra proposals would move. Advanced. | |
| indel_max_size | No | largest single-cut indel modeled either side of the cut — ICE's own CLI default is 20. In bp. Advanced. |
Output Schema
| Name | Required | Description | Default |
|---|---|---|---|
| iceD | Yes | ICE-D, an independent discordance-based read on the same trace — a second opinion rather than a restatement | |
| checks | Yes | TIDE once per guide and tracy's breakpoint call on the same pair, reported beside ICE and never averaged into it; tracy's `status` says whether it agrees with ICE's top sizes | |
| hdrPct | Yes | the HDR percentage, when a `donor` was given | |
| report | Yes | the whole result, including ICE's own notes and warnings | |
| iceScore | Yes | the headline ICE score: the edited fraction of the population, 0-100 | |
| perGuide | Yes | each guide's own answer: its cut (control base, from 1), the share edited there, its indel spectrum at that cut alone, and the alleles edited at it and another cut | |
| rSquared | Yes | how well the fitted mixture explains the edited trace. A high ICE score with a poor fit is not a result, and this is the number that says so | |
| spectrum | Yes | the indel-size histogram ICE publishes, every size from -2x to +1x `indel_max_size` INCLUDING the zeros, so the spectrum's shape is visible and not only its peaks | |
| baseEdits | Yes | with `base_editing`, each fitted substitution (protospacer position, control base, change, share, refit interval), the range of the pool carrying any, and the notes on phasing and near-cut calls; null otherwise | |
| inseparable | Yes | groups of reported alleles this trace cannot tell apart (their expected traces correlate above a variance inflation factor of 5), each with its summed share and 95% interval; the split inside a group is not measured | |
| contributions | Yes | each proposed edit with its relative abundance, most abundant first | |
| knockoutScore | Yes | the fraction carrying a frameshift or a 21+ bp indel — the number a knockout experiment is actually asking for, which is NOT the same as the edit fraction |