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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.
SUBMITTER: Denoulet M
PROVIDER: S-EPMC9846423 | biostudies-literature | 2023 Jan
REPOSITORIES: biostudies-literature
Denoulet Marie M Brulé Mathilde M Anquez François F Vincent Audrey A Schnipper Julie J Adriaenssens Eric E Toillon Robert-Alain RA Le Bourhis Xuefen X Lagadec Chann C
Bioinformatics (Oxford, England) 20230101 1
<h4>Motivation</h4>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 th ...[more]