ChIP with reference exogenous genome (ChIP-Rx) is widely used to study histone modification changes across different biological conditions. A key step in the bioinformatics analysis of this data is calculating the normalization factors, which vary from the standard ChIP-seq pipelines. Choosing and applying the appropriate normalization method is crucial for interpreting the biological results. However, a comprehensive pipeline for complete ChIP-Rx data analysis is lacking. To address these challenges, we introduce SpikeFlow, an integrated Snakemake workflow that combines features from various existing tools to streamline ChIP-Rx data processing and enhance usability. SpikeFlow automates spike-in data scaling and provides multiple normalization options. It also performs peak calling and differential analysis with distinct modalities, enabling the detection of enrichment regions for histone modifications and transcription factor binding. Our workflow runs in-depth quality control at all the processing steps and generates an analysis report with tables and graphs to facilitate results interpretation. We validated the pipeline by performing a comparative analysis with DiffBind and SpikChIP, demonstrating robust performances in various biological models. By combining diverse functionalities into a single platform, SpikeFlow aims to simplify ChIP-Rx data analysis for the research community.

SpikeFlow: automated and flexible analysis of ChIP-Seq data with spike-in control / Bressan, Davide; Fernández-Pérez, Daniel; Romanel, Alessandro; Chiacchiera, Fulvio. - In: NAR GENOMICS AND BIOINFORMATICS. - ISSN 2631-9268. - 6:3(2024), pp. 1-9. [10.1093/nargab/lqae118]

SpikeFlow: automated and flexible analysis of ChIP-Seq data with spike-in control

Bressan, Davide
Primo
;
Romanel, Alessandro;Chiacchiera, Fulvio
Ultimo
2024-01-01

Abstract

ChIP with reference exogenous genome (ChIP-Rx) is widely used to study histone modification changes across different biological conditions. A key step in the bioinformatics analysis of this data is calculating the normalization factors, which vary from the standard ChIP-seq pipelines. Choosing and applying the appropriate normalization method is crucial for interpreting the biological results. However, a comprehensive pipeline for complete ChIP-Rx data analysis is lacking. To address these challenges, we introduce SpikeFlow, an integrated Snakemake workflow that combines features from various existing tools to streamline ChIP-Rx data processing and enhance usability. SpikeFlow automates spike-in data scaling and provides multiple normalization options. It also performs peak calling and differential analysis with distinct modalities, enabling the detection of enrichment regions for histone modifications and transcription factor binding. Our workflow runs in-depth quality control at all the processing steps and generates an analysis report with tables and graphs to facilitate results interpretation. We validated the pipeline by performing a comparative analysis with DiffBind and SpikChIP, demonstrating robust performances in various biological models. By combining diverse functionalities into a single platform, SpikeFlow aims to simplify ChIP-Rx data analysis for the research community.
2024
3
Bressan, Davide; Fernández-Pérez, Daniel; Romanel, Alessandro; Chiacchiera, Fulvio
SpikeFlow: automated and flexible analysis of ChIP-Seq data with spike-in control / Bressan, Davide; Fernández-Pérez, Daniel; Romanel, Alessandro; Chiacchiera, Fulvio. - In: NAR GENOMICS AND BIOINFORMATICS. - ISSN 2631-9268. - 6:3(2024), pp. 1-9. [10.1093/nargab/lqae118]
File in questo prodotto:
File Dimensione Formato  
lqae118.pdf

accesso aperto

Tipologia: Versione editoriale (Publisher’s layout)
Licenza: Creative commons
Dimensione 1.9 MB
Formato Adobe PDF
1.9 MB Adobe PDF Visualizza/Apri

I documenti in IRIS sono protetti da copyright e tutti i diritti sono riservati, salvo diversa indicazione

Utilizza questo identificativo per citare o creare un link a questo documento: https://hdl.handle.net/11572/425450
Citazioni
  • ???jsp.display-item.citation.pmc??? 0
  • Scopus 0
  • ???jsp.display-item.citation.isi??? ND
social impact