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
FFPE samples often suffer from low quality RNA inputs, i.e. lots of degraded RNA, which often leads to pronounced 3' bias and sometimes dramatically reduced library complexity (i.e., only few genes were captured).

You should make sure to check the gene body coverages, exon coverages and library complexity (e.g. using [QoRTs](https://hartleys.github.io/QoRTs/)) because they may differ quite significantly from the fresh samples and may influence the types of comparison you can do.

Some nice assessments of the impact of degradation were done by [Schuierer et al., 2017](https://bmcgenomics.biomedcentral.com/articles/10.1186/s12864-017-3827-y) and [Li et al., 2014](https://www.ncbi.nlm.nih.gov/pubmed/25150837).