This repository describes the FISH Omics Format - Chromatin Tracing (FOF-CT), a community data format designed for capturing and exchanging the results of both ball-and-stick and volumetric Chromatin Tracing experiments (Dekker et al., 2023) that was initially produced within the context of the 4D Nucleome (4DN) project.
The format consists of a series of 15 tables with different degrees of requirements (see below).
- 12 tables are shared among FOF-bas-CT and FOF-vol-CT.
- 3 additional tables are specific for FOF-vol-CT.
The full list of tables and instructions on how to use them can be found at: https://fish-omics-format.readthedocs.io/.
The image below provides a schematic representation of 15 tables composing the FOF-CT. FOF-CT is a modular format designed to capture Chromatin Tracing data from two experiment modalities: Ball-and-Stick (bas) and Volumetric (vol). Tables are represented as color-coded boxes (3 red bas primary tables; 9 grey tables shared across both modalities; 3 blue vol-specific tables). The figure indicates each table's index number and short name in the upper-right corner. In addition, depicted is whether tables are required (triple line), conditionally required (double line), recommended (thick single line) or optional (single line). (Figure credit: Sarah Aufmkolk).
