DNA Methylation Sequencing Analysis Central Document

This will be my working document to connect all the datasets and different analysis pipelines together.

Projects

• Porties astreoides Thermal Transplant Molecular
  • How does pervious bleaching events impact adult and larval coral DNA methyation patters?
  • How does parental thermal history influence coral larval DNA methylation patterns and phenotypes?
• Crassostrea virginica nutition multiomic integration
  • How does nutirition enrichment alter the gut microbiome, gene expression, and DNA methylation patterns of the eastern oyster Crassostrea virginica?

While Genome Bisulfite library prepration

Whole genome bisulfite sequencing (WGBS) is an approach to obtain single base-pair resolution of DNA methylation within your sample. I have developed a library prepration protocol with the Zymo Pico Methyl Seq kit for the coral Porites astreoides linked here.

Bioinformatic pipelines

• DNA methylation QC and Quantification
  • This workflow describes how to use NF-core Methylseq to quanitfy methylation from raw reads, filter for 5X or 10X coverage, and prepare data for further analyses in R.
  • The HPC workflow is linked here
• DNA Methylation Characterization
  • This workflow describes how to characterize DNA methylation in various genomic features
  • The HPC workflow is linked here
  • The R workflow is linked here
• SNP extraction from Whole Genome Bisulfite Sequencing (WGBS) data
  • BS-SNPer workflow is linked here
  • Bis-SNP workflow is linked here
  • EpiDiverse workflow is linked here
• Plotting, Statsitics, WGCNA, Functional enrichment
  • This R script is linked here