ABSP: an automated R tool to efficiently analyze region-specific CpG methylation from bisulfite sequencing PCR - Archive ouverte HAL Accéder directement au contenu
Article Dans Une Revue Bioinformatics Année : 2023

ABSP: an automated R tool to efficiently analyze region-specific CpG methylation from bisulfite sequencing PCR

(1, 2) , , (3) , , (4) , (5) , (1) , (1) , (6)
1
2
3
4
5
6

Résumé

Abstract Motivation Nowadays, epigenetic gene regulations are studied in each part of the biology, from embryonic development to diseases such as cancers and neurodegenerative disorders. Currently, to quantify and compare CpG methylation levels of a specific region of interest, the most accessible technique is the Bisulfite Sequencing PCR (BSP). However, no existing user-friendly tool is able to analyze data from all approaches of BSP. Therefore, the most convenient way to process results from the direct sequencing of PCR products (direct-BSP) is to manually analyze the chromatogram traces, which is a repetitive and prone to error task. Results Here, we implement a new R-based tool, called ABSP for Analysis of Bisulfite Sequencing PCR, providing a complete analytic process of both direct-BSP and cloning-BSP data. It uses the raw sequencing trace files (.ab1) as input to compute and compare CpG methylation percentages. It is fully automated and includes a user-friendly interface as a built-in R shiny app, quality control steps, and generates publication-ready graphics. Availability and implementation The ABSP tool and associated data are available on GitHub at https://github.com/ABSP-methylation-tool/ABSP. Supplementary information Supplementary data are available at Bioinformatics online.

Dates et versions

hal-03936715 , version 1 (12-01-2023)

Identifiants

Citer

Marie Denoulet, Mathilde Brulé, François Anquez, Audrey Vincent, Julie Schnipper, et al.. ABSP: an automated R tool to efficiently analyze region-specific CpG methylation from bisulfite sequencing PCR. Bioinformatics, 2023, ⟨10.1093/bioinformatics/btad008⟩. ⟨hal-03936715⟩
0 Consultations
0 Téléchargements

Altmetric

Partager

Gmail Facebook Twitter LinkedIn More