Single-Cell Hi-C Analysis Workflow with Pairtools.
Methods Mol Biol
; 2856: 241-262, 2025.
Article
em En
| MEDLINE
| ID: mdl-39283456
ABSTRACT
Single-cell Hi-C (scHi-C) is a collection of protocols for studying genomic interactions within individual cells. Although data analysis for scHi-C resembles data analysis for bulk Hi-C, the unique challenges of scHi-C, such as high noise and protocol-specific biases, require specialized data processing strategies. In this tutorial chapter, we focus on using pairtools, a suite of tools optimized for scHi-C data, demonstrating its application on a Drosophila snHi-C dataset. While centered on pairtools for snHi-C data, the principles outlined are applicable across scHi-C variants with minor adjustments. This educational chapter aims to guide researchers in using open-source tools for scHi-C analysis, emphasizing critical steps of contact pair extraction, detection of ligation junctions, filtration, and deduplication.
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Base de dados:
MEDLINE
Assunto principal:
Software
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Genômica
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Fluxo de Trabalho
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Análise de Célula Única
Idioma:
En
Ano de publicação:
2025
Tipo de documento:
Article