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.

 

 

 
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