The DNA methylation haplotype (mHap) format and mHapTools.
Bioinformatics
; 37(24): 4892-4894, 2021 12 11.
Article
em En
| MEDLINE
| ID: mdl-34179956
ABSTRACT
SUMMARY:
Bisulfite sequencing (BS-seq) is currently the gold standard for measuring genome-wide DNA methylation profiles at single-nucleotide resolution. Most analyses focus on mean CpG methylation and ignore methylation states on the same DNA fragments [DNA methylation haplotypes (mHaps)]. Here, we propose mHap, a simple DNA mHap format for storing DNA BS-seq data. This format reduces the size of a BAM file by 40- to 140-fold while retaining complete read-level CpG methylation information. It is also compatible with the Tabix tool for fast and random access. We implemented a command-line tool, mHapTools, for converting BAM/SAM files from existing platforms to mHap files as well as post-processing DNA methylation data in mHap format. With this tool, we processed all publicly available human reduced representation bisulfite sequencing data and provided these data as a comprehensive mHap database. AVAILABILITY AND IMPLEMENTATION https//jiantaoshi.github.io/mHap/index.html. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
Texto completo:
1
Bases de dados:
MEDLINE
Assunto principal:
Software
/
Metilação de DNA
Limite:
Humans
Idioma:
En
Revista:
Bioinformatics
Assunto da revista:
INFORMATICA MEDICA
Ano de publicação:
2021
Tipo de documento:
Article
País de afiliação:
China