Bioinformatics Services

All Bioinformatics Core analyses start 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). 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.

Available Pipelines

Analysis	Services
Whole Genome / Exome (WGS/WES) Sequencing	Quality control of fastq files Variant calling (SNVs/INDELs) Copy number (CN) analysis
Bulk RNA-seq	Quality control of fastq files Quality control of sequencing libraries RLE boxplots, Library density plots, Sample-vs-sample correlations, MA-plots Dimensionality reduction and visualization Principal components analysis (PCA) and unsupervised clustering (heatmap) Differential expression (DE) analysis Volcano and MA plot output for each experimental contrast Results spreadsheet Gene set testing Over-representation analysis (Gene ontology)
ChIP-seq / CUT&RUN	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 Differential Abundance (DA) testing Volcano and MA plot output for each experimental contrast Motif analysis
Bulk ATAC-seq	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
PRO-seq	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)	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	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	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)

Fees

Estimated cost per sample for bulk type analysis:

Samples	Hours	Price
6	4	$1,000
9	6	$1,500
12	8	$2,000
15	10	$2,500
25	12	$3,000
>25		Contact for quote

Estimated cost per single-cell type analysis:

Samples	Hours	Price
6	8	$2,000
9	10	$2,500
12	12	$3,000
15	14	$3,500
25	16	$4,000
>25		Contact for quote

Estimated cost also includes a one-hour meeting with the bioinformatics team member(s) to review results. Any additional analysis outside this scope of work will be billed hourly.