The custom services provided by CGPM may include but are not limited to RNA-seq, ChIP-seq, DNA methylation, DNA variation, metagenomics, CRISPR Screening. Since estimating the cost of a bioinformatics project is usually quite difficult, we offer two different ways of working with us. For small, routine projects (e.g. standard RNA-seq analysis), we charge based on a fixed fee schedule which can be found below. For large projects, we charge based on the amount of effort. We will estimate how much effort for each project and notify you when we officially initiate your project.
RNAseq Analysis
Gene counts generation: $200 setup + $40/sample, $25~30/sample if sample size over 20.
Statistical analysis: $250 setup + $50/sample, $35~40/sample if sample size over 20.
Deliverables:
Alignment Files in BAM format
Gene / Transcript Expression Level File in MS Excel format
BigWig File For count visualization in Integrative Genomics Viewer (IGV)
List of Differentially Expressed Gene / Transcript in MS Excel format (includes integration into Geneious software [License held by the Department of Biological Science, FSU] for downstream analysis)
List of enrichment GO terms for differentially expressed genes in MS Excel format
Volcano plots for pairwise analysis of each sample
Barplot for enriched GO terms for differentially expressed genes in PNG/PDF format
Chip-Seq Analysis
$300 setup + $50/sample for alignment and basic quality assessment (mapped reads, multiply mapped reads, number of duplicates, coverage correlation etc,), $35~40/sample if sample size over 20.
$25/sample extra for peak calling.
$300 setup + $65/sample for differential binding statistical analysis, $40~45/sample if sample size over 20.
Deliverables:
Alignment Files in BAM format
List of Peaks in Excel format
List of Annotated differential Peaks in Excel format
List of GO terms for peak-associated genes in Excel format
BigWig File For Peaks visualization in Integrative Genomics Viewer (IGV)
Barplot for enriched GO terms for peak-associated genes in PNG/PDF format
CRISPR Screening Analysis
Gene counts generation: $200 setup + $40/sample, $25~30/sample if sample size over 20.
$25/sample extra for performance analysis (fold change of essential and non-essential sgRNAs, correlation analysis, precision recall curve etc,).
Statistical analysis: $250 setup + $50/sample, $35~40/sample if sample size over 20.
Deliverables:
Alignment files in BAM format
The counts of each gene in the CRISPR library in MS Excel format
List of synergistic and suppressor genes in MS Excel format
List of figures in PNG/PDF format for the quality of the screen
Barplot and boxplot for reads distribution
The plot of the distribution of observed fold-changes of gRNA targeting essential and nonessential genes
Heat map of sample correlations
Precision-recall curves
DNA Methylation Analysis
Reads mapping and methylation calls: $200 setup + $30/sample
DMRs and DMCs identification: $300 setup + $50/sample
Deliverables:
Alignment Files in BAM format (Human and Lambda if applicable)
List of Annotated CpG Methylation Sites in Text/Excel format
List of Annotated CHG and CHH Methylation Sites in Text format
Bisulfite conversion rate of Lambda (if applicable)
Boxplot of DNA methylation for differential methylation levels between samples
Methylation heatmap for grouping and visualization of samples
DNAseq Analysis
Somatic variants identification: $300 setup + $50/sample, include genome alignment, alignment co-cleaning, somatic variant calling etc, $35~40/sample if sample size over 20.
Deliverables:
Alignment Files in BAM format
VCF file with high-confidence somatic variants
Metagenomics analysis
Demultiplexing and quality filtering, OTU picking, taxonomic assignment: $200 setup + $40/sample. $25~30/sample if sample size over 20.
Functional annotation, pathway reconstruction: $300 setup + $50/sample, $35~40/sample if sample size over 20.
Deliverables (whole genome)
De novo Assembly Files (raw files and contigs) in various formats
BLAST files (raw) in native BLAST format
Taxonomy Tree
Species Composition in Excel format
Deliverables (16S)
Joined Paired-End Reads in FASTA format
Operational Taxonomic Unit (OTU) Table
Taxonomy Summary
Results of Alpha Diversity (diversity within the sample groups)
Results of Beta Diversity (comparison of diversity between the groups of sample)
