GenePattern Team Blog

Visualizer launching problems and other Java related issues

Posted on Wednesday, July 17, 2013 at 11:23AM by David Eby

UPDATE MARCH 17, 2017 : Java applet visualizers no longer work in any browser. Please click here to read the blog post.

We have recently been getting many reports from users having trouble launching GenePattern visualizers - HeatMapViewer, HierarchicalClusteringViewer, PCAViewer and so on - especially on Mac computers.  There have also been reports of issues with running the GenePattern installer and using the File Uploader.  If you are experiencing any of these problems the following suggestions might help you.  These components use the Java platform and the problems all seem to trace to a recent set of Java updates from Oracle and Apple.  In particular, many problem reports come from users with Java 7 Update 25 on Mac OS X 10.7 and above or Java 6 Update 51 on OS X 10.6.  Issues have been reported with other combinations, but less frequently. 
These are the latest updates of Java available for these platforms and came out within the last...

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GenePattern 3.6

Posted on Thursday, May 30, 2013 at 02:11PM by GenePattern Team

GenePattern 3.6 contains several new features and fixes.

New Features

Updated Job Submit Page

In GenePattern 3.6, the job submit page (the page that appears when you select a module or pipeline) has been revised for ease of use.  The user interface has been streamlined with clearer drag--and-drop targets, updated buttons and other UI elements, and reorganized module information in the header.

Improved File Input

We have improved file input to modules and pipelines in a number of ways:

  • You can drag-and-drop your input files from your desktop or from the Job Results, Uploads, and GenomeSpace tabs
  • There is a new upload progress bar that appears after you click the Run button if you are directly uploading files from your client file system (via drag-and-drop from the local file system or the Upload File button)

Drag-and-drop File Lists

We have implemented the ability to drag-and-drop/upload multiple files for a single module run; this provides...

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RNA-seq QC in GenePattern

Posted on Tuesday, March 05, 2013 at 11:28AM by The GenePattern Team


After aligning and/or assembling your RNA-seq data, it is important to take a closer look at the content of those result files before continuing with further analysis; in part, because the results of that investigation may, in fact, point you toward how you should best analyze your data.

Specifically in GenePattern, modules are provided to calculate such Quality Control (QC) metrics as: Depth of Coverage, Continuity of Coverage, Duplication Rate, Expression Rates, Strand Specificity, and GC content, among others.

Having these sorts of metrics can help to prevent or better understand common RNA-seq errors stemming from such sources as: read length, quality of data, sample prep, or number of reads in the data.

Modules in GP

  • Picard.AddOrReplaceReadGroups
  • SortSam
  • Picard.CreateSequenceDictionary
  • Picard.ReorderSam
  • Picard.MarkDuplicates
  • SAMtools.FastaIndex
  • RNAseqMetrics

The following decision diagram illustrates a suggested workflow. This workflow is discussed in further detail...

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