We normalize with the housekeeping gene in the qPCR anlaysis. But why we are not normalizing the NGS data with some housekeeping genes for differential gene expression?
If you are sequencing genome DNA (NGS), then there is no expression data. If you are using RNA-seq, then you have to normalize for library size, GC %, transcript length, and other factors.
Article Selecting between-sample RNA-Seq normalization methods from ...
Yes for RNA-seq analysis.Thank you Katie A S Burnette for your reply. But why we are normalizing with housekeeping gene in qpcr and why not in RNA-seq analysis?
Swathi Divakar , If your reads counts are in different scales, then only you need to do normalization. During NGS analysis, your RNA-seq read counts matrix transformed into a meaningful comparison of counts across your sample so we dont need to do normalization. But sometime people use different RNA-seq data generated from different platform, then your read counts will be in different scales. In that case in RNA-seq also definitely you need to go for normalization.
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