Skip to main page content
Access keys NCBI Homepage MyNCBI Homepage Main Content Main Navigation
. 2016 Oct 15;32(20):3190-3192.
doi: 10.1093/bioinformatics/btw368. Epub 2016 Jun 17.

TADtool: Visual Parameter Identification for TAD-calling Algorithms

Affiliations
Free PMC article

TADtool: Visual Parameter Identification for TAD-calling Algorithms

Kai Kruse et al. Bioinformatics. .
Free PMC article

Abstract

Eukaryotic genomes are hierarchically organized into topologically associating domains (TADs). The computational identification of these domains and their associated properties critically depends on the choice of suitable parameters of TAD-calling algorithms. To reduce the element of trial-and-error in parameter selection, we have developed TADtool: an interactive plot to find robust TAD-calling parameters with immediate visual feedback. TADtool allows the direct export of TADs called with a chosen set of parameters for two of the most common TAD calling algorithms: directionality and insulation index. It can be used as an intuitive, standalone application or as a Python package for maximum flexibility.

Availability and implementation: TADtool is available as a Python package from GitHub (https://github.com/vaquerizaslab/tadtool) or can be installed directly via PyPI, the Python package index (tadtool).

Contact: kai.kruse@mpi-muenster.mpg.de, jmv@mpi-muenster.mpg.deSupplementary information: Supplementary data are available at Bioinformatics online.

Figures

Fig. 1.
Fig. 1.
(A–D) TADtool window. (A) Hi-C plot, (B) TADs (black bars) called with current window size (WS: 2.5 × 105) and cutoff (2.7 × 10-3), (C) insulation index plot for current window size, (D) heatmap of insulation index for all window sizes. (E) Modifying TAD-calling parameters changes the identified TADs. (F) TADs called from Dixon et al. (2012) data with window size used in the original publication (bottom) and modified (top)

Similar articles

See all similar articles

Cited by 14 articles

See all "Cited by" articles

References

    1. Crane E. et al. (2015) Condensin-driven remodelling of X chromosome topology during dosage compensation. Nature, 523, 240–244. - PMC - PubMed
    1. Dekker J. et al. (2002) Capturing chromosome conformation. Science, 295, 1306–1311. - PubMed
    1. Dixon J.R. et al. (2012) Topological domains in mammalian genomes identified by analysis of chromatin interactions. Nature, 485, 376–380. - PMC - PubMed
    1. Fraser J. et al. (2015) Hierarchical folding and reorganization of chromosomes are linked to transcriptional changes in cellular differentiation. Mol. Syst. Biol., 11, 14. - PMC - PubMed
    1. Hou C. et al. (2012) Gene density, transcription, and insulators contribute to the partition of the drosophila genome into physical domains. Mol. Cell, 48, 471–484. - PMC - PubMed
Feedback