Last week I was trying to get trhough Nature Protocol: Transcript-level expression analysis of RNA-seq experiments with HISAT, StringTie and Ballgown. https://www.ncbi.nlm.nih.gov/pubmed/27560171 . I downloaded the required softwares and tried to follow it with the data from the protocol. However when I got to the Ballgown part in R software I noticed that any gene was differentially expressed. The highets " q value" that I got when I sorted them it was 0.5 or 0.6. I didnt get any "q value" less than 0.05 . Looked up the steps before (hisat and stringtie) and it is ok... Did someone have already tried this protocol with data provided by Nature and got the same results ???