TADEvoDrosophila

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TADEvoDrosophila

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Code for TAD_SV project

TADEvoDrosophila 최신버젼 다운로드

최종 버전 다운로드 (.zip)

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# Topologically Associating Domains (TADs) in Drosophila species

Topologically associating domains (TADs) are recently identified as functional and physical units of 3D genome organization, which were thought to play vital roles in genome function (e.g. gene regulation), strucuture (e.g. chromosomal rearrangements) and evolution. This spacial features were originally discovered in Hi-C contact maps as domains within which DNA sequences physically contact each other more densely than they are outside (Sexton et al. 2012; Dixon et al. 2012). TADs or TAD-like domains have been widely characterized across the kingdom of the life, suggesting they represent a conserved feature of genome organization.

This collection of command-line scrips is to run the methods we used in our work "https://www.biorxiv.org/content/10.1101/2020.05.13.094516v1" for analyses:

(1):   TAD annotation using Armatus, Arrowhead (Juicer package), and HiCExplorer;

(2):   TAD conservation analysis;

(3):   Gene expression analysis;

(4):   Identification of chromosomal rearrangement breakpoints using whole genome alignment based on LASTZ/CHAIN/NET/NETSYNTENY tools;

(5):   Genome assembly-based Structural variants(SVs) identification;

(6):   TADs versus SVs analysis.

TADEvoDrosophila

TADEvoDrosophila 최신버젼 다운로드

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