Custom Bioinformatics – complete and customizable solutions
All services include bioinformatics support to ensure you receive the analysis you need!
Services & Packages
Basic Service Packages include raw data alignment, variant calling (differential methylation or SNP detection), and gene/locus annotation.
Full Service Packages offer additional down-stream bioinformatics processing and statistical analysis specifically tailored to fit your needs. Comparisons can be performed between samples as well as groups of samples.
Do you have Next-Gen sequencing data that you need analyzed?
Zymo Research offers complete bioinformatics solutions to fulfill your needs. Whether it is whole-genome bisulfite sequencing, ChIP-Seq, or RNA-Seq data, we can help make sense of your overwhelming data sets. We use established as well as customizable bioinformatics pipelines to transform raw sequence data into manageable and interpretable figures and data sets. Simply provide the raw (FASTQ) or aligned (SAM or BAM) data and we will provide you with your desired downstream analyses.
Click on a figure below for more information
Two kinds of UCSC Genome Browser tracks are provided for visualization of methylation data: the Methylation track and the Read track. The Methylation track indicates methylation ratios (percent methylated) at each site, and the Read track alignment to the reference genome. Simply copy and paste provided tracks into the UCSC Genome Browser to access gene annotations, SNPs, repetitive DNA elements, and comparison to results of the ENCODE project for each region.
For each CpG covered in the assay, the Result Table indicates chromosomal position and the associated gene name, promoter region and/or CpG island annotations. It is the best way for you to discover methylation changes at specific CpG sites. Using these annotations, you can quickly review regions of interest. This single-nucleotide resolution CpG analysis differs from other approaches that provide average signals for enriched regions showing high levels of DNA methylation making it more sensitive and quantitative to identify methylated cytosines in DNA.
The hexbin plot is an updated version of the scatterplot that is better suited for analysis of very large data sets. It indicates the correlation between two samples with the Pearson's R correlation coefficient displayed at the top. Colors, at the indicated location on the plot, represent point densities with Red indicating points comprised from many values and Blue showing points from only a few values.
The heatmap provides statistical grouping and easy visualization of samples according to DNA methylation levels. In this heatmap (above), Red represents CpG sites that are 0% methylated and Yellow sites with 100% methylation. Dendrograms of hierarchical clustering based on methylation ratios help determine which samples share similar methylation patterns in specific regions of their DNA.
Genomic Region Pie Chart
The Genomic Region Pie Chart categorizes every CpG site analyzed into promoter, exon, intron, or intergenic regions allowing for easy visualization/determination of the genomic regions covered by the analysis.
Region Coverage Pie Chart
The Region Coverage Pie Chart indicates the read coverage (fold) for an indicated region, in this case, for CpG islands. Region coverage pie charts are available for promoter, gene body, exon, intron, and intergenic regions.
Methylation Level Boxplot
The boxplot displays the mean and distribution of DNA methylation within a sample. The boxplot (above) shows the 2nd quartile (mean) as a yellow line, and 1st quartile and 3rd quartile as the bottom and upper bounds of the box, respectively.
The Methylation Overview plot displays the DNA methylation ratio (percent methylated) across the entire genome for quick analysis of DNA methylation levels across all genomic regions.
Read Coverage Plot
The Read Coverage Plot shows the read coverage on a log scale across entire genome for easy visualization of the extent of coverage in the regions analyzed.