DNAnexus and Differential Expression Analysis/Visualization

[JMo]

Hey all,

Has anyone utilized DNAnexus to analyze RNA-Seq data? They allow you to analyze 10 samples for free and I was able to get my RNA-Seq data mapped and aligned, but oddly they do not support differential expression or statistical analysis on their website? The files I got back have RPKM and RMS-normalized RPKM values along with the gene names and IDs. Are there any programs I can plug these values into to perform the differential expression and statistical analysis on my replicates and perform visualizations?

This is my first time performing RNA-Seq and am still trying to keep my head above water. Thanks for any help!

JMo

[rpeters]

You may want to look at the tools provided by Partek. You can start with raw data, or aligned files, or RPKM values to look at differentially expressed genes, alternative splicing, allele specific expression, novel regions. There are a number of tools to perform statistical analysis and differential expression using either RPKM or raw read quantification values(other transformations are also available). There are options to handle replicates with a wide variety of experiment designs, including multi-factor and mixed model designs.

Additionally, there are a multitude of visualizations to get at the biology and to view the data as well (Hierarchical Clustering, Profile Views, etc) with an extensive data mining toolkit.

[kbhit]

HandsFree

You may want to look at a system called HandsFree (http://cm.jefferson.edu/HandsFreee) that gives the ability to analyze the large datasets that next generation sequencing platforms generate. From a quick look at their website it can map and analyze RNA-Seq, Exome-seq, DNA-seq, and ChIP-Seq data

http://jefferson.edu/web_options/tags/news_fullstory.cfm?articleID=568