Resources and popular analyses with price estimates
Planning to do an experiment using high-throughput data? Here are some handy resources to help you plan your reserach project:
Application of single-cell and bulk RNA sequencing in onco-immunology.
Systematic assessment of tumor purity and its clinical implications.
Comprehensive assessment of somatic copy number variation calling using next-generation data.
Examples of common analyses at BCF with price estimations:
Below you will find some examples of commonly requested analysis with BCF. The standard analysis approach with corresponding deliverables are listed together with hands-on time, delivery time and approximate price excluding VAT. Please note that none of the prices and time-estimations are scalable in a linear fashion. Price and delivery time is dependent on data amount, data quality, sensitive/not sensitive data, custom requests etc.
Single-cell analysis
For a standard analysis of two single-cell samples:
- Overall gene expression analysis
- Clustering
- Cell-type annotation
- Data integration of the two samples
- Marker gene detection
Deliverables:
- QC plots
- UMAP and t-SNE plots with and without cell cycle regression
- Heatmap of marker genes
- Marker gene table with differentially expressed genes
- Bar plots with number of cells from each sample per cluster
- Complete R object with annotations
- Analysis report from BCF
Time usage and price estimation:
16 hrs hands on, 4 weeks delivery, 13 600 NOK ex. VAT.
Price and time usage is not scalable in a linear fashion. Please contact us for a quote tailored to your project.
Bulk RNA differential expression
Pairwise differential expression analysis for 24 bulk mRNA samples (sensitive) with less than 10 conditions:
- Overall QC of raw data
- Read mapping to reference and filtering
- Feature counting
- Count normalization
- Differential expression - pairwise for given conditions
- Pathway analysis
Deliverables:
- All generated data and corresponding scripts
- PCA plot
- Tables of up/down-regulated genes for each pairwise comparison
- Volcano plots for each pairwise comparison
- Heatmap of normalised expression values
- Pathway analysis for each pairwise comparison
- Analysis report from BCF
Time usage and price estimation:
45 hrs hands on, 6 weeks delivery, 38 250 NOK ex. VAT.
Price and time usage is not scalable in a linear fashion. Please contact us for a quote tailored to your project.
Variant calling tumor-normal pairs
Variant calling for 100 exome sequenced tumor-normal pairs (sensitive):
- Somatic variant calling - small variants using two different callers
- Somatic variant calling - structural and copy number variants
- Intersect of dual small variant output
- Annotation of all variants
Deliverables:
- BAM files from reference alignment
- All results from all callers used
- VCF file with intersected small variants
- Annotation report of variants both HTML and TSV
- Analysis report from BCF
Time usage and price estimation:
100 hrs hands on, 6 weeks delivery, 85 000 NOK ex. VAT.
Price and time usage is not scalable in a linear fashion. Please contact us for a quote tailored to your project.