Quality check, alignment of sequencing data to reference genome, and identification of methylated or hydroxymethylated regions. Provided files include FastQC reports, alignment files in BAM format, and peak files in BED format.
Additional analysis on request:
Differential methylation analysis:
Identification of differential methylation or hydroxymethylation between samples based on previously identified MeDIPseq/hMeDIP-seq peaks.
Annotation with genomic regions:
Annotation of MeDIP-seq/hMeDIP-Seq peaks with genomic regions such as introns, exons, enhancers (when available), promoters, intergenic regions.
Gene ontology terms analysis:
Enrichment analysis on gene sets. Gene Ontology terms that are overrepresented in differentially bound regions may indicate the underlying biological processes involved.
Identify biochemical pathways in which genes associated with differentially methylated regions (or individual differentially methylated CpGs) may be overrepresented.
Visualization of specific genomic regions:
Visualization of results (i.e. sequencing data, peaks) at specific genomic regions (e.g. genes, promoters) in publication-ready images (human, mouse, rat).