Bioinformatics

Available analysis workflow for:

  • RNA-seq
  • ChIP-seq
  • ATAC-seq
  • WES/WGE
  • Reduced Representation Bisulfite Sequencing (RRBS)
  • Microbiome metagenomics (16S sequencing)
  • scRNA-seq
  • scATAC-seq

Example Standard outputs:

RNA-seq
  • QC report
  • File (bigwig) for trace visualization on UCSC or IGV; BAM alignment file available on request
  • Raw gene count table
  • List of differentially expressed genes with their expression fold change and FDR-corrected p-values
  • 3 visualizations: PCA, heatmap, volcano plot
  • List of pathways

RRBS

  • QC report
  • BAM alignment file (when requested)
  • Complete table of methylation for all detected CpG site
  • List of differentially methylated CpG sites with p-values (FDR-corrected)
  • Visualizations: PCA plot, heatmap, volcano plot
  • For significantly differentially methylated CpGs list of pathways of nearby genes

scRNA-seq

  • QC report
  • Barcoded BAM alignment file available (for GEO)
  • UMI/Cell count table
  • tSNE or UMAP clustering for subpopulations
  • List of differentially expressed genes with their expression fold change and FDR-corrected p-values based on either clustering or experimental conditions (for both additional 2 hour charge). If no subpopulations are identified based on clustering, differential expression will be performed based on experimental conditions.
  • 2 visualizations: heatmap, volcano plot
  • List of pathways


Fees:    Starting at $250/hour for bioinformatics analysis.


Estimated cost per sample for bulk analysis

Sample

Hours

Cost

6

4

$1,000

9

6

$1,500

12

8

$2,000

15

10

$2,500

25

12

$3,000

More than 25 samples, contact for quote

  

Estimated cost per sample for single cell type analysis

Sample

Hours

Cost

6

8

$2,000

9

10

$2,500

12

12

$3,000

15

14

$3,500

25

16

$4,000

More than 25 samples, 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.

Contact:

Gennaro Calendo - Email