Raise your hand if you’ve just about had it with storing your raw genomics data on unreliable portable hard-drives or messy difficult to manage shared file servers?
Want to assemble a collection of sequenced sample datasets to analyze? Well, you have to track down the files, resurrect the annotations, and hope that it all still works when you send it out for analysis. It’s hard enough to run a simple kindred or case/control analysis – never mind larger meta-analysis or cohort studies that may span multiple investigators and sequencing platforms.
Well, there’s good news: Managing and analyzing your genomics data doesn’t have to be so difficult. With the right combination of data management platform and analysis applications, you can easily prepare and analyze both private and public samples – all without lengthy delays waiting for assistance from overworked bioinformatics core staff.
In this blog post, we’ll walk through how to use the new integration of QIAGEN’s Ingenuity applications with the InSilico DB open data management platform. When we’re done, you’ll know exactly how to launch a free preview in Ingenuity iReport™ or Ingenuity Variant Analysis™ from both public and private samples in InSilico DB. Ready? Let’s dive in!
4 steps to a Free Ingenuity Preview from InSilico DB
1) Register for a free InSilico DB and Ingenuity Variant Analysis and/or iReport account
Visit both InSilico DB and Ingenuity to sign up for free accounts if you haven’t already done so. You will need both accounts to maximize the benefit. Tip: Use the same email for each to simplify data transfers, and make sure to sign up for Variant Analysis and/or iReport, depending on your interest.
2) Check out an InSilico DB public dataset or upload your own private dataset
The good folks at InSilico have been kind enough to assemble a collection of over 250,000 samples, complete with annotations and genomic measurements. Datasets have been pre-processed and formatted so you can quickly start your analysis with Ingenuity applications. InSilico has also manually curated public datasets related to particular areas of research interest.
To extend the discovery capabilities, you can upload your own private datasets and combine them with available public data to run larger analyses. After all, new scientific discoveries often require comparing genomic information from many samples, in light of which have particular conditions or diseases.
By combining your private samples with other well characterized genomic samples, you can identify publishable insights faster than by just analyzing them alone. Check out this helpful post for how to upload a private dataset to InSilico DB.
3) Select the Ingenuity® tab for one-click access
The Ingenuity® tab offers access to hundreds of datasets, ready for instant export to Ingenuity applications. You can filter for just those datasets compatible with Variant Analysis or iReport.
Currently Ingenuity iReport is listed as an option for the RNA-Seq data type and Ingenuity Variant Analysis is shown as an option for DNA-Seq. Click the Variant Analysis or iReport button to send the necessary files to your Ingenuity account for analysis. Tip: Make sure to check, change or complete any of the text fields before sending the dataset to Ingenuity.
4) Follow the prompts and login to the Ingenuity application to view your results
After a minute or so you will see a notification window telling you that your dataset has been exported to the Ingenuity application of your choice. You may need to log in again separately if you have not already done so. While the analysis or report is being prepared in Ingenuity, you will see a progress screen that will redirect to the results as soon as they become available.
Click the button to open the Ingenuity application and view a free preview of your results.
The whole process may take a few minutes, particularly for datasets with larger file sizes. You will receive an email with a link to the results when complete.