ABSP: an automated R tool to efficiently analyze region-specific CpG methylation from bisulfite sequencing PCR.
Bioinformatics
; 39(1)2023 01 01.
Article
in En
| MEDLINE
| ID: mdl-36629453
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.
Full text:
1
Database:
MEDLINE
Main subject:
Sulfites
/
DNA Methylation
Language:
En
Journal:
Bioinformatics
Year:
2023
Type:
Article
Affiliation country:
France