Alignment & variants

Sanger indel spectrum (editing efficiency without NGS)

Quantify CRISPR editing from a pair of Sanger traces — an unedited control and the edited pool — by decomposing the edited trace onto shifted copies of the control. Returns the indel spectrum (how much of the pool carries each insertion or deletion size), the unedited fraction, and the R² of the decomposition, which is the number that says whether the model fits your traces at all. Non-negative least squares, so no allele is ever assigned a negative share. Does not work for base editing, which makes a mixed base rather than a shift.

post/sanger_indel_spectrum

Request

  • Base URL: https://seqbench.com/api/v1
  • URL: https://seqbench.com/api/v1/sanger_indel_spectrum
  • Auth: none required

Request body

controlBasesstring required

Base calls of the UNEDITED control read.

editedBasesstring required

Base calls of the edited pool's read.

cutPositionnumber required

1-based position of the expected cut, in CONTROL read coordinates.

maxIndelnumber

Largest indel to include in the basis, in bp (max 20). Every shift from −maxIndel to +maxIndel is fitted.

windowLengthnumber

Bases downstream of the cut used for the decomposition (20-300). Longer is better conditioned but needs more clean read.

guardnumber

Bases skipped immediately after the cut, where the trace is least reliable.

offsetnumber

Override the alignment offset between the reads. By default it is found from the base calls upstream of the cut, which is reported back along with the identity achieved.

Response

Tool ran successfully.

okunknown required
toolstring required

The tool slug that ran.

resultobject required

Tool-specific output object. Its shape depends on the tool — call GET /{tool} or see the docs for each tool's fields.

Example response

{
  "provenance": {
    "apiVersion": "1.1.0"
  }
}

Changes

No recorded changes to this operation across all 1 revision of this API.