I performed a large scale methylation analysis by RRBS-Seq on Infinium Human Methylation 450K BeadChip platform with generated raw data in FASTQ format. What are the main steps to do the bioinformatic analysis?
Thanks.
There's a nice update to RnBeads (2.0) that was just published. Knowledge of R programming is a must, but otherwise very straightforward. Please message me if you have specific questions!
The paper: Article RnBeads 2.0: Comprehensive analysis of DNA methylation data
There's a nice update to RnBeads (2.0) that was just published. Knowledge of R programming is a must, but otherwise very straightforward. Please message me if you have specific questions!
The paper: Article RnBeads 2.0: Comprehensive analysis of DNA methylation data
methylKit is an R package for DNA methylation analysis and annotation from high-throughput bisulfite sequencing. The package is designed to deal with sequencing data from RRBS and its variants, but also target-capture methods and whole genome bisulfite sequencing. It also has functions to analyze base-pair resolution 5hmC data from experimental protocols such as oxBS-Seq and TAB-Seq.
Did you have experience with some network-based algorithms, such as the weighted human DNA methylation PPI network ?
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