Genomic Data Science Core Services

Prices are valid from July 1, 2023 – June 30, 2024

RNA-seq pre-processing

Internal rate: $225
External rate: $396

Pre-processing of a standard RNA-seq datasets for species with an existing well annotated reference genome(e.g. human, mouse). Includes read pre-processing, alignment, quantification, and a detailed quality control report (up to 30 samples).

RNA-seq analysis (Two-factor)

Internal rate: $1200
External rate: $2112

Downstream analysis of a standard pre-processed RNA-seq dataset. Includes exploratory data analyses (e.g. PCA and hierarchical clustering), differential expression analysis for a standard two-factor experiment, and preliminary pathway/gene ontology analyses. Output includes tables of differential expression results, in addition to numerous publication-quality figures. This analysis is limited to a single comparison.

RNA-seq Analysis (Multi-factor)

Internal rate: $1800
External rate: $3168

As above for a standard RNA-seq two-factor experiment, however, involves multi-factor comparisons, for example between multiple treatment groups. If the number of groups or experimental design is especially complicated, additional time at the hourly rate may be required to complete the analysis. This analysis can incorporate up to 5 comparisons, additional comparisons will be charged the hourly rate.

Cut and Run analysis 

Internal rate: $2250
External rate: $3960

Analysis of CUT&RUN data for species with an existing well annotated reference genome. Data pre-processing includes read trimming, alignment, peak calling, peak reproducibility analysis, and an extensive quality control assessment. Downstream analyses include peak annotation, differential binding, and motif enrichment. Further analyses, such as pathway analysis or integration with other genomic data types, will be charged at the hourly rate (see below) (up to 30 samples).

ATAC-seq analysis (pre-processing & QC)

Internal rate: $225
External rate: $396

Analysis of ATAC-seq dataset for species with an existing well annotated reference genome. Includes read trimming, alignment, peak calling, peak reproducibility analysis, and an extensive quality control assessment. Downstream analyses such as peak annotation, differential accessibility, motif enrichment, or integration with RNA-seq data, will be charged at the hourly rate (see below) (up to 30 samples).

Variant Calling (SNPs & Indels only)

Internal rate: $600
External rate: $1056

Includes read pre-processing, quality control, alignment, variant calling, detailed filtering of called variants (including quality filters, and filtering against a matched-normal or population reference for somatic datasets), and basic annotation. Includes WES, WGS, or gene-specific panels. Note: does not include detailed review of specific variants, which is suggested for variants of interest (up to 30 samples).

DNA Methylation analysis (arrays)

Internal rate: $450
External rate: $792

Includes pre-processing of array files (IDATs), quality control (including QC report), normalization, background correction, and basic exploratory data analyses (e.g. hierarchical clustering) (up to 30 samples). Downstream analyses will be charged at the hourly rate.

Genome assembly and annotation

Internal rate: $600
External rate: $1056

Includes pre-processing of fastq files, quality control assessment, and assembly of genomes and genome assembly (Up to 10 samples). Genome annotation will provide annotation of coding sequences for assembled contigs (up to 10 samples). Additional downstream analyses will be charged at the hourly rate.

Metagenome assembly and annotation

Internal rate: $900
External rate: $1584

Includes pre-processing of fastq files, quality control assessment, and assembly of metagenomes and metagenome assembly (Up to 10 samples). Metagenome annotation will provide taxonomy assignment and annotation of coding sequences for assembled contigs (up to 10 samples). Additional downstream analyses will be charged at the hourly rate.

Hourly data analysis:

Internal hourly rate: $75
External hourly rate: $132

Includes any work that is not included in the above categories, such as integrative genomics analysis, analysis of publicly available data, single-cell experiments, custom projects, or project consultation. Unique datasets may require some analysis that falls under the hourly rate to occur before analysis using a standardized pipeline. Please contact us for an estimate if your experiment is not included in any of these categories.

Bioinformatics office hours on zoom:

By appointment, contact DataAnalyticsCore@groups.dartmouth.edu