Data Analysis / Bioinformatics Support
The Genomics Resources Core Facility provides data analysis and bioinformatics support for RNA sequencing, DNA sequencing, single-cell sequencing, chromatin profiling, immune repertoire sequencing, long-read sequencing, and Olink protein profiling data.
Our goal is to help investigators generate data that are suitable for the intended analysis, evaluate data quality, identify meaningful biological patterns, and communicate results clearly for research, grants, presentations, and publications.
How Can We Support Your Project?
Our support can begin before data generation and continue through data processing, customized analysis, result review, and grant/publication-related support.
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We can discuss the biological question and intended comparisons before data generation to help choose an appropriate sequencing and analysis strategy. From a data analysis perspective, we help identify design or technical issues that may affect downstream analysis.
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We process data using established workflows and platform-specific pipelines, including Illumina demultiplexing and FASTQ generation, 10x Genomics Cell Ranger workflows, PacBio SMRT Link workflows, and other standard processing pipelines when applicable.
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We provide analysis beyond standard pipeline output, such as project-specific quality assessment, statistical comparison, clustering or annotation, pathway analysis, data integration, and visualization based on the biological question.
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We help investigators review analysis results, distinguish biological signals from potential technical artifacts, understand major findings and limitations, and prepare figures or analysis summaries for grants, abstracts, presentations, and manuscripts when included in the project scope.
Supported Applications
We support standard and customized analysis for the following application areas. If your project does not fit one of these categories, please contact us to discuss whether we can support it.
RNA Sequencing
Support for bulk RNA sequencing and related transcriptomic studies, including standard processing, differential expression analysis, pathway or gene set analysis, visualization, and interpretation support based on the experimental design.
DNA Sequencing
Support for whole-genome, whole-exome, targeted panel, and amplicon sequencing projects, including standard processing, quality review, coverage assessment, variant-related analysis, copy-number or structural-variant analysis when appropriate, and project-specific interpretation support.
Single-cell Sequencing
Support for 10x Genomics single-cell and single-nucleus sequencing datasets, including gene expression, CITE-seq or other barcode-tagged measurements, single-cell ATAC-seq, 10x Multiome, and single-cell V(D)J data when applicable.
Chromatin Profiling
Support for ATAC-seq, CUT&RUN, CUT&Tag, and related chromatin profiling assays, including standard processing, peak-based analysis, differential accessibility or binding analysis, visualization, and interpretation support when appropriate.
Long-read Sequencing
Support for PacBio long-read sequencing projects, including whole-genome sequencing, full-length transcriptome analysis, and full-length TCR/BCR sequencing when applicable. Analysis includes platform-specific processing, quality assessment, alignment, transcript or isoform-level analysis, variant or structural-variant analysis, and project-specific interpretation support depending on study design.
Immune Repertoire Sequencing
Support for TCR/BCR repertoire and single-cell V(D)J datasets, including V(D)J processing, clonotype analysis, repertoire-level review, clonal expansion analysis, and integration with single-cell gene expression data when available.
Olink Data Analysis
Support for Olink protein profiling datasets, including quality review, normalization review, group comparison, visualization, pathway or functional analysis when appropriate, and interpretation support based on project goals.
Custom Bioinformatics Support
Some projects require analysis beyond standard workflows. We may support project-specific analysis needs, including data integration, re-analysis of existing datasets, troubleshooting unexpected results, advanced visualization, and grant/publication-related analysis support depending on project scope.
Request Support
Contact us to discuss your project. Early discussion is recommended when planning a new study, choosing between sequencing strategies, working with complex experimental designs, or requesting customized analysis.
Schedule a Consultation
After the project scope is discussed, analysis requests can be submitted through iLab for project tracking, billing, and official processing.