Packaged Bioinformatics Services
The bioinformatics team has developed reproducible bioinformatic analysis pipelines for common analyses with common experimental designs. These highly automated analysis pipelines are offered as packages.
To engage these services, we ask that you (1) create a user profile (this step will only need to be completed for first time requesters) and (2) complete our intake form. This form collects essential details for tailoring the analysis to your unique study, including but not limited to:
- Project title: A concise title capturing the focus of your research
- Study description: A summary outlining the scope, objectives, and context of your study
- Project funding details: Specification of funding source and budget allocation for bioinformatic services
- Requested project timeline: Information about your project’s timeline, including any specific deadlines or milestones
Jump to our available services:
ATAC-seq analysis
Whole genome/whole exome sequencing analysis
RNA-seq analysis
Detailed description
Example statement of work
Example project report
Pipeline codebase
What does it do?
The ATAC-seq analysis service offered by the bioinformatics team provides a comprehensive exploration of genome-wide chromatin accessibility. This technique, known as assay for transposase-accessible chromatin using sequencing (ATAC-seq), is designed to profile and understand the dynamic interplay between chromatin structure and gene regulation.
What kinds of questions does it answer?
The ATAC-seq analysis service addresses questions related to chromatin accessibility in your research. It helps uncover insights into how genes are regulated by assessing changes in chromatin structure. Specifically, the analysis can reveal alterations in accessibility, providing valuable information about regulatory mechanisms and their impact on gene expression.
When we start the project, you will provide us with:
- The primary data
- A manifest mapping the data files to the physical specimens
What you will receive from us
- Upon receipt of the intake form, we will schedule a time to meet and discuss the project in detail. In a following meeting, we will put together a statement of work document detailing the project scope, expectations, and outcomes.
- Final communication includes an email with the processed data and a synopsis summarizing key findings in a non-technical manner. This synopsis aims to provide a clear understanding of the implications of the chromatin accessibility changes observed in the context of your specific research.
Whole genome/whole exome sequencing analysis
Detailed description
Example statement of work
Pipeline codebase
What does it do?
Whole genome sequencing (WGS) and whole exome sequencing (WES) are methods for characterizing variability in an individual’s genome. They use next generation sequencing technology to determine genetic sequence. Analysis of these data is computationally intensive because it requires alignment of millions of sequenced “reads” to a reference genome and using a statistical model to identify genomic loci of interest. This processing is run on our high-performance compute environment.
What is the difference between WGS and WES?
WGS and WES use the same underlying technology but are tuned to deliver information on different parts of the genome. WGS sequences DNA across the entirety of the genome, while WES preferentially sequences the approximately 1% of the protein coding part of the genome. This allows additional sequencing depth on the parts of the genome that are most likely to contain variants that affect health, at the expense of coverage of non-exonic DNA.
What kinds of questions does it answer?
WES and WGS provide information on the approximately 3 million genetic locations that vary between individuals. We use these tools clinically and in research projects to help determine the relationship between genotype and disease. WES and WGS can also be used to study differences in genomic architecture in tumors versus healthy tissue.
When we start the project, you will provide us with:
- The primary data
- A sample sheet that maps the data files to the physical specimens and the relationship among the samples, if they are not unrelated
What you will reveive from us
- We will supply aligned BAM files for each sample and VCF files detailing called variants and their annotation.
Detailed description
Example statement of work
Example project report
Pipeline codebase
What does it do?
RNA-sequencing (RNA-seq) is a high-throughput sequencing technique designed to provide insight into the transcriptome (gene expression) of a sample. The RNA-seq analysis service offered by the bioinformatics team provides a comprehensive exploration of gene expression and enriched biological pathways.
What kinds of questions does it answer?
RNA-seq is mainly used to identify differentially expressed genes and differentially enriched biological pathways between sample groups. In addition to gene expression profiling, RNA-seq can be used to identify known and novel transcript isoforms, alternative splicing events, single nucleotide variants and small insertions/deletions (indels), and gene fusions.
When we start the project, you will provide us with:
- The primary data
- A manifest mapping the data files to the physical specimens
What you will receive from us
- Upon receipt of the intake form, we will schedule a time to meet and discuss the project in detail. Following this meeting, we will put together a statement of work document detailing the project scope, expectations, and outcomes.
- Final communication includes an email with the processed data and a synopsis summarizing key findings in a non-technical manner. This synopsis aims to provide a clear understanding of the implications of the gene expression changes observed in the context of your specific research.
