Posted on Wednesday, July 17, 2013 at 11:23AM by David Eby
Posted on Thursday, May 30, 2013 at 02:11PM by GenePattern Team
GenePattern 3.6 contains several new features and fixes.
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.
We have improved file input to modules and pipelines in a number of ways:
We have implemented the ability to drag-and-drop/upload multiple files for a single module run; this provides...
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.
The following decision diagram illustrates a suggested workflow. This workflow is discussed in further detail...