We have extensive experience with a wide variety of analyses, including:
- Bulk RNA-Seq
- ChIP-Seq
- ATAC-Seq
- TRAP-Seq
- Multi-omics integration (Mixomics, sPLS-DA)
- *New* VISIUM Spatial single-cell RNAseq
- 10X Single-cell RNA-seq
- Pathway Analysis with award-winning iPathwayGuide pro software
- Exome/Whole Genome variant calling and filtering with DRAGEN BIO-IT genomics engine (on-premise)
- Metabolomics analysis
- MinION and ONT long read transcriptomics, isoform DE testing, variation, and methylation
- and many more...
We can also support your lab in other ways:
- Grant review and letters of support
- Figure and table generation for manuscripts
- Experimental design review and consulting
We are also able to research, adapt and perform a variety of more custom or emerging techniques. We are happy to meet to discuss the feasibility of developing or implementing any bioinformatics analysis. Please submit an inquiry to the IIHG Bioinformatics Division with a brief description of the project or question and the principal investigator’s name and contact information at iihg-bioinformatics@uiowa.edu.
We recommend that you contact us prior to beginning any experiments requiring bioinformatics analyses to help ensure success of the project. Our input on experiment design can usually save you money and improve the chances of success in many types of NGS experiments.
Pricing
As the quantity and complexity of datasets increase exponentially, so does the complexity of the analysis methods available and the questions that can be asked of the data. Please budget a significant fraction of your total spending on the library prep and sequencing data generation for the analysis of those data.
Routine RNA-seq:
A typical RNA-seq project might be billed as follows:
- $500 project setup fee (inital consultation, copy data, merge fastqs, setup pipeline, troubleshoot, review QC)
- $75 per sample (pipeline run to generate BAM files and counts, exploratory PCA, DEG analysis)
- $100 per pathway analysis report (iPathwayGuide software)
- $500 / NCBI GEO data cataloging and upload for GEO accession creation and GEO access management (optional)
- Follow up consultation meetings are available (Included)
- 3 yrs data archiving and backup on IIHG servers (Included)
-- Discounts on the "per-sample" price can be applied for large projects (>48 samples).
-- Methods sections and results figures for manuscripts can be produced to help you publish your project (billed hourly)
Example project: 20 sample mouse RNA-seq analysis
$500 project setup fee + ($75 per sample fee x 20) + ($100 pathway analysis reports x 3): Total = $2300
Custom projects:
If you need custom analysis work, please contact us directly for a custom quote for your project.
Downloading your data from Genomics:
If you use Linux, you can follow these instructions:
1) Login to your linux terminal and navigate to the directory where you want to store your data
2) Locate the HTTP URL for your dataset (should be in the email you received from IIHG Genomics)
3) Type the following command: "wget -r -v --no-parent my_http_url_link_from_genomics" (where you substitute the actual link)
4) The download should begin and will take several minutes.
5) After the download is complete, you will need to move all your fastq files to one folder. So create a new folder called "raw' with the command "mkdir raw"
6) Then search for all of the fastq files you just downloaded and move them to the "raw" folder with: "find . -type f -name "*.fastq.gz" -exec mv {} raw \;"
7) Now you should have all the fastq files in one folder called "raw." You can use this folder as input to a pipeline or merge fastq files together if they were split across lanes.
If you use Mac OS, you can follow the above directions but you first need to install "wget" on your machine using "Brew":
https://formulae.brew.sh/formula/wget#default
If you use PC, you should consider switching to Mac or Linux.