RNAseq analysis of FFPE samples

Question

[Ron]

Hi all,

I wanted to know what kind of QC checks can be done for RNA access samples so that can be used for analysis ,similar to regular RNAseq data sequenced by Truseq kits(polyA). Since RNA access is for low quality RNA FFPE, what analysis can be done to check if we can use the data from them?

I have looked at the mapping reads,FASTQC reports, and the overall statistics from STAR which look fine. Some of my colleagues have mentioned its hard to detect fusions from RNA access as well.

Overall,is there any other idea to confirm/check that could determine if we can use these samples and compare them with good quality samples if needed ?

Thanks, Ron