quantify_base_editing
Read-only
Quantify BASE EDITING from a single Sanger trace, with no control read — the EditR method (Kluesner et al. 2018), ported and graded against the authors' own R.
Input Schema
| Name | Required | Description | Default |
|---|---|---|---|
| guide | Yes | the protospacer, 5'→3', without the PAM. Matched exactly against the read's own base calls; the coordinates it lands on come back in the result. | |
| trim3 | No | last base of the read the background model may be fitted on, 1-based inclusive. Pair it with `trim5`. | |
| trim5 | No | first base of the read the background model may be fitted on, 1-based inclusive. GIVE BOTH BOUNDS OR NEITHER — upstream errors on a lone one rather than filling the other in. Left unset, upstream's automatic rule runs: drop the first 20 bases, then drop every base whose total peak height is under a tenth of the mean of what is left. The window is an INPUT to the answer, not a view: it is what the noise is estimated from, so tightening it lowers the cut-off. | |
| _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. | |
| _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. | |
| document | No | which trace file to read: its name (`read_F.ab1`) or its project file id. LEAVE IT EMPTY to run on the chromatogram tab that is open. A file id is project-specific, so a template ships this unset. | |
| guide_end | No | the other end of an explicit placement, 1-based inclusive. Pair it with `guide_start`. | |
| guide_start | No | place the guide yourself, 1-based inclusive in the read's own base calls, instead of matching it exactly. GIVE BOTH BOUNDS OR NEITHER. This is what a read carrying a sequencing error inside the protospacer needs: the analysis tests the bases you point at rather than refusing the read. | |
| p_value_cutoff | No | a base is called as edited when its share of the position's signal clears this trace's own noise model at this probability. EditR's own default is 0.01. | |
| guide_is_reverse_complement | No | search for the guide's reverse complement. A C→T edit on the guide strand then reads as G→A in the result. |
Output Schema
| Name | Required | Description | Default |
|---|---|---|---|
| calls | Yes | every significant call: { guidePosition, index, guideBase, base, percent, pValue }, biggest first | |
| edited | Yes | whether ANY base of the guide carries a non-reference signal above this trace's own noise. Wire it into a gate | |
| report | Yes | the whole run: every guide position with all four base percentages and p-values, the four fitted noise models and their cut-off lines. This is what makes a negative checkable — 'no editing' and 'the model could never have fired' look identical without it | |
| topChange | Yes | the biggest call as `reference→edited`, e.g. `C→T`. Empty when there is none | |
| guideStart | Yes | 1-based position in the read's own base calls where the guide was found — what a canvas needs to draw it | |
| topPercent | Yes | its share of that position's total peak height, 0–100 | |
| topPosition | Yes | the guide position (1-based) of the biggest call, or 0 when there is none |