Truseq Stranded Total RNA and NEBNext Ultra II Directional RNA library prep kit

Question

[deniz]

Hi, Has anyone try to analyze the RNA-seq data from Illumina Truseq Stranded Total RNA kit and NEBNext Ultra II Directional RNA library prep kit together? If so, can you please give some suggestion about the normalization of the data which acquired from these two different library prep kits?

I have only tumor samples for Truseq Stranded Total RNA kit. And for NEBNext Ultra II Directional RNA library prep kit I have the same type of tumor samples and also control samples.

Best, DK

Answer 1

[Anna]

Hi,

if you encounter batch effects with your samples due to using different library preps, you can have a go at removing unwanted variation using Ruvseq.

https://bioconductor.org/packages/release/bioc/html/RUVSeq.html

A great lecture on the effect of using Ruvseq:

https://vimeo.com/299777276