Hello! I have a question of FFPE samples for NGS.
Are the fresh/frozen samples superior than FFPE samples for NGS? What I know now is that DNA from FFPE samples are more fragmented than common DNAs. Are there some other characters could distinguish these types of tissue in terms of NGS(here I mean RNA-Seq and Targeted DNA sequencing)?
One intertesting fact for me is usually the DNA 260/280 absorbance value 1.8-2.0 is considered as "pure", and for "pure" RNA the value is like 2.0-2.2. But for some commercial kits, DNA 260/280 value of 1.7-1.9 is enough, and for RNA 260/280 value is OK if between 1.9-2.1.
I'm wondering if the paraffin will necessarily decrease the quality of DNA/RNA? And generally, will a slighter higher than normal 260/230 value, i.g.2.3-2.4, will affect the reliability of RNA-Seq and Targeted DNA sequencing?
You guys are always my bioinformatic hero. Short and clear answers are preferred firstly. Then bomb me with links or reference. Thank you. Have a nice day.