With the rapidly evolving landscape of high-throughput sequencing technologies and advancements in various 'omics' protocols, a vast amount of sequence data is at our disposal, presenting both a challenge and an opportunity. Embracing this data deluge with excitement, the CAT Core at UCSF is dedicated to providing unwavering support to researchers at every stage of their projects, from initial planning to comprehensive data analysis.
In March of 2024, the CAT Core added Bioinformatics services to support and enhance the value of sequencing data generated across our platforms. Our bioinformatics team has decades of experience and is equipped to help researchers maximize insights from complex datasets. As our service offerings continue to grow, we will provide updated information on specific applications and expertise available.
Bioinformatics Service Offerings
Our bioinformatics services cover a broad range of analyses tailored to support sequencing applications across multiple platforms, including PacBio and Illumina. Below are some of the key services we currently provide:
Project Consultation and Experimental Design
Collaborate with our bioinformatics experts to design optimal experiments that align with your research goals. We assist with determining technology use, sequencing depth, appropriate controls, and analytical approaches to ensure robust and meaningful data.
Bioinformatics Analysis
Our bioinformatics services cover a comprehensive range of standard analyses to support diverse sequencing applications. We assist with data processing, quality control, alignment, and downstream analyses, including differential expression, isoform detection, variant calling, community profiling, assembly, and methylation profiling. Our team has experience across multiple sequencing technologies and applications, providing tailored solutions to meet the research needs of UCSF’s community.
For every project, we ensure high-quality, reproducible analysis pipelines with detailed documentation, facilitating a seamless transition from data acquisition to interpretation.
Custom Analysis and Algorithmic Development
For projects requiring specialized analysis, novel algorithms, or advanced data exploration, we offer custom analysis and algorithm development services. Our bioinformatics team can work collaboratively to design and implement unique approaches that extend beyond standard workflows, creating bespoke solutions for cutting-edge research needs.
Custom services include:
- Development of novel algorithms and pipelines for unique research questions.
- Custom data integration across different 'omics' platforms or species.
- Development of specialized visualization tools for high-dimensional data.
Whether your project requires unique analytical approaches or novel pipeline development, our team is equipped to help bring your vision to reality.
Data Visualization and Interpretation
We help bring data to life with customized visualizations tailored to convey key findings. Whether for presentations, publications, or internal reports, our team can create figures and plots to showcase your results effectively.
Bioinformatics Workshops
Our meticulously designed bioinformatic workshops offer participants immersive, hands-on experiences that equip them with the knowledge and skills necessary to design and execute successful bioinformatics and genomics experiments. Led by a seasoned Bioinformatics Core expert, these workshops delve into both the theoretical underpinnings and practical applications of a diverse array of genomic experiments, including but not limited to genome assembly, RNA-Seq analysis, epigenetic studies, single-cell RNA-Seq techniques, long-read technologies and more.
How to Get Started
For researchers interested in bioinformatics services, we highly recommend an initial consultation to discuss your project's goals and requirements. if you'd like to email your questions, please send a message to catbioinformatics[at]@ucsf.edu. Our team will work closely with you to develop a tailored analysis plan, with recommendations on optimal sequencing workflows, appropriate data processing, and analysis pipelines.
Stay tuned as we continue to expand our bioinformatics offerings to serve UCSF's dynamic research community better. We look forward to supporting your projects and helping turn complex data into valuable insights.