Best RNA-Seq Analytical Pipeline to use - opinions ?

[gendxdoc]

I am starting a project to examine differences in gene expression, across multiple regions of the brain -- from individuals with and without (controls) a neurodegenerative disorder.

My plan was to use TopHat2/Cufflinks/etc. to identify significant differences in expression amongst affecteds and controls for each brain region. However, I'm hearing from colleagues that there are better alternatives for RNA-Seq analysis, or at least that's what they're hearing -- although when I ask them what the alternate pipelines are - they can't remember the tool names.

In addition to understanding expression differences -- I would also like to examine differential allelic expression.

You're opinions about which pipelines to use for these applications would be appreciated ! If there are newer, better pipelines or tools to use -- please let me know.

Thanks

[Krish_143]

1) Tophat-Cufflinks-CummeRbund.
2) EdgeR

[colindaven]

I have had very promising and (I hope) biologically meaningful results from edgeR.