This is an example bisulfite sequencing data analysis workflow, starting from quality control and alignment steps for .fastq files. We worked with reduced representation bisulfite sequencing (RRBS) data but most steps are applicable to WGBS as well. The anonymized RRBS data are available in Array Express, accession code E-MTAB-10530 (release date June 6th 2022).
This repository is intended as:
-
Documentation of the data preprocessing and analysis steps of these two papers: (1) Laajala et al. "Permutation-based significance analysis reduces the type 1 error rate in bisulfite sequencing data analysis of human umbilical cord blood samples", Epigenetics 2022, doi: 10.1080/15592294.2022.2044127 and (2) Laajala et al. "Umbilical cord blood DNA methylation in children who later develop type 1 diabetes", Diabetologia 2022, doi: 10.1007/s00125-022-05726-1.
-
A resource for other people who analyze bisulfite sequencing data and are fluent in R. Interactive testing of the code is strongly recommended.
Laajala et al. "Permutation-based significance analysis reduces the type 1 error rate in bisulfite sequencing data analysis of human umbilical cord blood samples", Epigenetics, 2022 Mar 4;1-20. doi: 10.1080/15592294.2022.2044127