Bioinformatics Services

Bioinformatic Analysis

All Bioinformatics Core analysis starts with standard quality control reporting of the raw sequenced reads. Depending on the assay performed, we offer a wide variety of standardized pipelines (see below). Expected results include:

• custom plots
• statistical analysis
• results spreadsheets
• reproducible code

We are also available for consulting before, during, and after project completion to assist in everything from experimental design and planning, to bespoke visualizations, and assistance with uploading of sequence data and results to NCBI GEO for publication. 

Whole Genome/Exome (WGS/WES) sequencing analysis Quality control of raw fastq files Variant calling (SNV/INDELS) Copy number (CN) analysis	ChIP-seq / CUT&RUN analysis Quality control of fastq files Quality control of sequencing libraries Peak calling / sliding window analysis Peak annotation Bigwig files of peaks for track browser visualization Dimensionality reduction and visualization Differential Abundance (DA) testing Volcano and MA plot output for each experimental contrast Motif analysis
Bulk ATAC-seq analysis Quality control of fastq files Quality control of sequencing libraries Fragment size distribution, library complexity, PT ratio, TSS enrichment Peak calling / sliding window analysis Peak annotation Bigwig files for track browser visualization Dimensionality reduction and visualization Differential Abundance (DA) testing Volcano and MA plot output for each experimental contrast Motif analysis	Bulk RNA-seq analysis Quality control of raw fastq files Quality control of sequencing library composition RLE boxplots, Library density plots, Sample-vs-sample correlations, MA-plots Dimensionality reduction and visualization  Principal components analysis and unsupervised clustering (heatmap) Differential expression (DE) analysis Volcano and MA plot output for each experimental contrast Results spreadsheet Gene set testing Over-representation testing (Gene ontology)
Pro-seq analysis Quality control of fastq files Quality control of sequencing libraries Bigwig files of enrichment for track browser visualization TSS enrichment profiles and heatmaps Promoter-proximal pause index calculation Dimensionality reduction and visualization Differential Pausing	Reduced representation bisulfite sequencing (RRBS) analysis Quality control of raw fastq files Quality control of sequencing library composition Dimensionality reduction and visualization  Differential methylation analysis Gene set testing Over-representation testing (Gene ontology)
Single-cell RNA-seq analysis Quality control of raw fastq files Quality control of sequencing library composition Dimensionality reduction and visualization UMAP / tSNE Clustering analysis Cell type prediction Differential expression analysis Cluster-level or pseudobulk Gene set testing Over-representation testing (Gene ontology)	Single-cell multiome analysis Quality control of raw fastq files Quality control of sequencing library composition Dimensionality reduction and visualization UMAP / tSNE Clustering analysis Cell type prediction Differential expression analysis Cluster-level or pseudobulk Differential abundance analysis Feature linkage Gene set testing Over-representation testing (Gene ontology)