Go Back   SEQanswers > Applications Forums > RNA Sequencing

Similar Threads
Thread Thread Starter Forum Replies Last Post
anyone with experience of using new RNA lib prep kit for FFPE samples on Novseq seraphin_IL Sample Prep / Library Generation 0 01-25-2019 02:02 PM
Illumina FFPE QC Kit for exome sequencing Amy S Sample Prep / Library Generation 1 10-16-2014 06:35 AM
ChIP-Seq library prep kit, Illumina vs Kapa biznatch Sample Prep / Library Generation 1 11-28-2013 02:25 AM
Can Truseq RNA kit compatiblity with Truseq exome-enrichment kit? gemzhanglinlin Sample Prep / Library Generation 0 07-22-2013 02:16 PM
NEBNext ChIP-Seq library prep kit vs Illumina TruSeq kit? ASL Sample Prep / Library Generation 1 04-10-2013 08:35 PM

Thread Tools
Old 05-21-2019, 02:24 AM   #1
not just another member
Location: Belgium

Join Date: Aug 2010
Posts: 264
Default RNA-Seq on FFPE samples : Illumina TruSeq RNA exome or Roch Kapa HMR kit


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 :


Roche Kapa HMR

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

Any experience with these kits with FFPE samples ?

Thank you
NicoBxl is offline   Reply With Quote
Old 11-02-2020, 04:24 PM   #2
Junior Member
Location: usa california

Join Date: Nov 2020
Posts: 1

similar situation here, also would like to know the answer.
Thank you!
karen201210 is offline   Reply With Quote
Old 11-04-2020, 06:44 AM   #3
Location: Illinois

Join Date: Oct 2014
Posts: 42

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.
jteeee2 is offline   Reply With Quote

ffpe, kapa, rna-seq, truseq rna

Thread Tools

Posting Rules
You may not post new threads
You may not post replies
You may not post attachments
You may not edit your posts

BB code is On
Smilies are On
[IMG] code is On
HTML code is Off

All times are GMT -8. The time now is 02:16 AM.

Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2021, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO