Overview

A UCSC CRISPR track is three files:

File

What it is

cas12a.bb

bigBed (bed9+) of on-target guides, one row per protospacer

crisprDetails.tab.gz

bgzip-compressed per-guide off-target lists

crisprDetails.tab.gz.gzi

the bgzip .gzi index (produced by bgzip -i)

The column schema, cas12aTargets.as, is a fixed autoSql file kept in the repo and passed to bedToBigBed at build time. It is not a per-genome output.

Each bigBed row stores a guide’s coordinates, color, on-target scores, off-target specificity, and an _offset: a byte offset into the uncompressed crisprDetails.tab. Clicking a guide makes the browser seek that offset (via the .gzi index) and render the off-target list. _offset = 0 means no list is stored, the guide is either non-unique or already perfectly specific (see Off-target records).

Cas12a specifics

  • PAM is 5’, 4 nt (TTTV), opposite end from Cas9’s 3’ NGG. V = A/C/G.

  • A guide site spans PAM(4) + spacer(23) = 27 nt; the spacer is the bigBed “thick” region.

  • We score with two CFD off-target matrices in one pass, enCas12a (WT) and AsCas12a/2xNLS.

The off-target asymmetry that drives the index

The guide PAM is TTTV (the strong, canonical set). The off-target index uses TTTN, because enCas12a also cleaves the weak TTTT PAM.

Note

Throughout, “specificity” is an aggregate over a guide’s per-off-target CFD scores: 1.0 = perfectly unique, lower = more / closer off-targets. On-target scores (DeepCpf1 and friends) are a separate axis predicting cutting efficiency.

References