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