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
1 answer
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:
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I would start with
vstfromDESeq2followed by plotting a PCA to see if these is a kit-batch-effect, probably it is. Do you have replicates from the same sample/group in each batch?Thank you for the comment. 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.