RNA-Seq on FFPE samples : Illumina TruSeq RNA exome or Roch Kapa HMR kit

[NicoBxl]

Hi,

I've ~300 FFPE samples to analyzed using RNA-Seq. I've two possibilities for the library prep depending on the sequencing center I will chose.

Either :

Illumina TruSeq RNA Exome : https://emea.illumina.com/content/il...na-access.html

or

Roche Kapa HMR

Both libraries will be sequenced at 2x100bp - 50M reads

Any experience with these kits with FFPE samples ?

Thank you

[karen201210]

similar situation here, also would like to know the answer.
Thank you!

[jteeee2]

Both are fine choices so the decision will likely come down to what sort of transcripts you are interested in looking at. The TruSeq RNA Exome kit is going to give you significantly higher coverage of coding transcripts but you will not have any non-coding RNA data to analyze. Depending on the starting RNA quality, the Roche Kapa HMR kit (or similar) will yield somewhere between 20-40% alignment rates to exonic regions.