mHapTk: a comprehensive toolkit for the analysis of DNA methylation haplotypes.
Bioinformatics
; 38(22): 5141-5143, 2022 11 15.
Article
in En
| MEDLINE
| ID: mdl-36179079
ABSTRACT
SUMMARY:
Bisulfite sequencing remains the gold standard technique to detect DNA methylation profiles at single-nucleotide resolution. The DNA methylation status of CpG sites on the same fragment represents a discrete methylation haplotype (mHap). The mHap-level metrics were demonstrated to be promising cancer biomarkers and explain more gene expression variation than average methylation. However, most existing tools focus on average methylation and neglect mHap patterns. Here, we present mHapTk, a comprehensive python toolkit for the analysis of DNA mHap. It calculates eight mHap-level summary statistics in predefined regions or across individual CpG in a genome-wide manner. It identifies methylation haplotype blocks, in which methylations of pairwise CpGs are tightly correlated. Furthermore, mHap patterns can be visualized with the built-in functions in mHapTk or external tools such as IGV and deepTools. AVAILABILITY AND IMPLEMENTATION https//jiantaoshi.github.io/mhaptk/index.html. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
Full text:
1
Collection:
01-internacional
Database:
MEDLINE
Main subject:
DNA Methylation
/
High-Throughput Nucleotide Sequencing
Language:
En
Journal:
Bioinformatics
Journal subject:
INFORMATICA MEDICA
Year:
2022
Document type:
Article
Affiliation country:
China