Hello,

I will analyze soon RNA-Seq samples build using a TruSeq RNA Exome (illumina) from FFPE. I've already a standard RNA-Seq pipleline that works well on fresh tissue ( RiboZero kits). Pipeline is a classic STAR-DESeq2 + additional post-hoc analysis (splicing, fusion, pathways, etc..). 

In this context, should I be carefull on some steps using capture-based RNA-Seq samples from FFPE samples ?

thank you
I would be interested to know if there are some criticals bias too !

A start in this Intro : https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5976456/