New RNA-Seq based expression estimation program, sleuth', was released today from Lior Pachter's group. This one challenges currently used 'count-based' methods for RNA-Seq data. Sleuth also accounts for biological and technical variation.
He raises a few good points that RNA-Seq based expression estimation becomes challenging since there is a biological variation of transcription within and between cells. Also, sometimes technical variations in a repeated sequencing experiment can overshadow the 'true' expression level changes.
https://liorpachter.wordpress.com/2015/08/17/a-sleuth-for-rna-seq/
software download: http://pachterlab.github.io/sleuth/
