Archive by Author | Eric Smith

Annotate your RNA-Seq data with NextBio Research

We’ve developed a new BaseSpace app named NextBio Annotates RNA-Seq that lets you ‘test-drive’ NextBio Research on your RNA-Seq data. With a few clicks, you can find how the most differentially expressed genes in your experiment are correlated with diseases, tissue types, public studies, and more.

NextBio Annotates RNA-Seq

NextBio Annotates RNA-Seq

 

When you run the Cufflinks Assembly and DE app on your RNA-Seq data, you receive a list of differentially expressed genes. What do these genes do? In what cell lines are they expressed? What drugs are they associated with? These are the questions that NextBio Research helps to answer.

When you run the NextBio Annotates RNA-Seq app, the most differentially expressed genes from your experiment are annotated via the NextBio Research API. The output report shows you how those genes are correlated with many public experiments. This is accomplished by the extensive curation of public data that has been performed by the NextBio curation team.

Example output from the NextBio Annotates RNA-Seq app

 

Of course this app gives just a taste of what NextBio Research can do. In the full version of the product, you can import data of many different types — not just RNA-Seq data. You can use the NextBio Correlation Engine to find how ranked lists of genes from your experiments compare to those in thousands of public experiments. If you’re interested, you can try the full version for free.

We hope this app shows you how NextBio Research can enrich your experiments, by easily annotating and correlating your data with curated public experiments.

IGV Genome Browser — Streamlined and Updated

We just released an important update to BaseSpace IGV that adds several new features and bug fixes.

Launch IGV from the App Store

Launch IGV from the App Store

First, we updated to Broad IGV version 2.3 (from version 2.1). This update includes many new useful features from The Broad Institute, which you can read about here.

IGV BaseSpace menu

We also improved the BaseSpace data browser within IGV. You can now select BaseSpace data to load into IGV from a separate window, which keeps the primary IGV window clean for analyzing sequencing data. The new data browser will open every time you launch IGV from BaseSpace. You can also access the browser from the ‘BaseSpace ‘ menu in IGV.

BaseSpace IGV data browser

Finally, we improved how BaseSpace IGV is launched and updated. After you launch IGV for the first time, we cache the downloaded files on your computer so that subsequent launches are very fast. When we release updates to IGV, these will be automatically downloaded on your next app launch. Also, if IGV is already open on your computer, launching from BaseSpace now adds the newly launched data into IGV.

We hope that these improvements will allow you to quickly and easily view your BaseSpace data in IGV.

Our First App — Broad’s IGV

We’re excited to announce our first app — the Broad’s Integrative Genomics Viewer (IGV). IGV brings the power of a rich genome browser to your BaseSpace data. It also shows you what launching apps will be like in BaseSpace.

BaseSpace Data in IGV

IGV is a fully featured genome browser that allows you to visualize your sequence data in great detail. It is a desktop application that can load data both from your local computer and over the Internet. We’ve modified IGV to display alignment and variant data from BaseSpace (BAM and VCF files). This allows you to perform variant analysis after launching Resequencing or Amplicon workflows in BaseSpace.

Launching the IGV App in BaseSpace

Launching IGV from BaseSpace is simple. After selecting IGV from the App Launcher, you’ll be asked for permission to allow IGV to read your BaseSpace data. Then IGV launches (your browser downloads a ‘jnlp’ file – in some browsers you may need to manually open this file). Launching IGV in BaseSpace is also context sensitive. When you’re viewing an analyzed Sample in BaseSpace and you launch IGV, the Sample will be highlighted in IGV. Currently, you can launch IGV in BaseSpace from the Sample Details page of an App Result.

Browsing BaseSpace Files in IGV

When you launch IGV, you’ll give the app permission to view everything in one of your Projects. We’ve added a file explorer to IGV so you can navigate your Project’s data within IGV. Only BAM and VCF files will show for now (i.e. alignments and variants). Just double click to load them into the browser (it’s best to load variants — the VCF files —  first to they don’t get hidden below an alignment track).

How did we develop the IGV app?

We developed the IGV app just as any developer will develop apps for BaseSpace. That is, we used the BaseSpace API to access BaseSpace data. We’ve released our version of the IGV app as open source on github – check it out to see how we used the API and add features if you wish. If you want to create your own apps with the BaseSpace API, check out our developer portal.

We hope you find the IGV app useful for analyzing your BaseSpace data. Let us know what you think! We’re excited to release IGV as our first app. Check back here for announcements about more apps to come.