tide_quantify_indels
Read-only
Quantify a CRISPR edit from a pair of Sanger traces by TIDE (Brinkman et al.) — the abundance of each indel SIZE in the sequenced population, with a p-value per size class, the total editing efficiency, the goodness of fit, and the base composition of the +1 insertion. This is a different question from crispr_quantify_edits, not a cheaper version of it: ICE fits a mixture of whole proposed alleles and names them, TIDE fits the control trace shifted by n bases and so reports how much of the population shifted by n, whatever allele carried it. Run both on the same pair when the two disagree about how much was edited — that disagreement is information about the read.
Input Schema
TableJSON Schema
| Name | Required | Description | Default |
|---|---|---|---|
| guide | Yes | the guide spacer, RNA accepted. TIDE decomposes around ONE break, so this is a single guide rather than a list — it is located in the control on either strand and the break is placed three bases 5-prime of the PAM. | |
| _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. | |
| control | Yes | the UNEDITED trace, by file name or id — every indel class is the control trace shifted, so this read IS the model. | |
| seq_end | No | last base of the READ to use, clamped down to the shorter of the two reads if it overruns. In bp. | |
| _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. | |
| max_shift | No | largest indel size modeled, in both directions. One basis function is fitted per size from -max_shift to +max_shift, so this bounds what can be reported at all. In bp. | |
| seq_start | No | first base of the READ to use. The start of a Sanger read is poor quality; upstream's own web app starts at 100. In bp. | |
| window_end | No | last base of the decomposed region. 0 = as far as the shorter read allows. In bp. Advanced. | |
| p_threshold | No | an indel class is called PRESENT below this p-value. A 0% class and a non-significant class are different answers, which is why this is a knob rather than a constant. Advanced. | |
| window_start | No | first base of the decomposed region. 0 asks the engine to place the window after the break itself, which is what upstream does when given no boundaries. In bp. Advanced. |
Output Schema
TableJSON Schema
| Name | Required | Description | Default |
|---|---|---|---|
| indels | Yes | every modeled size from -max_shift to +max_shift with its percentage, p-value and whether it cleared the threshold — INCLUDING the classes that did not, so the spectrum has a shape and not only peaks | |
| report | Yes | the whole result, including the window corrections upstream raises as warnings | |
| rSquared | Yes | goodness of fit of the whole decomposition. Every percentage below is already scaled by it, so a low fit shrinks the classes rather than flagging them | |
| breaksite | Yes | the base the break was placed at, three bases 5-prime of the PAM. Every window in the result is positioned against it | |
| efficiency | Yes | total editing efficiency: the R-squared-scaled signal in every non-zero indel class, 0-100. Not the same quantity as an ICE score — wire them into a comparison rather than treating either as the number | |
| aberrantSignal | Yes | the four means TIDE's own quality checklist is read from: control and sample, before and after the break. A sample already aberrant BEFORE the break is a sequencing problem rather than an edit, and this is the pair of numbers that says so | |
| insertionBases | Yes | base composition of the +1 insertion as percentages in A, C, G, T order — the readout ICE cannot produce. Null when there is no significant +1 class, which is the common case and not an error; `insertionNote` then says why in upstream’s own words | |
| significantIndels | Yes | the classes that cleared p_threshold, excluding the unmodified class — what a gate should read |