house keeping genes for RNA-seq

Question

[kanwarjag]

Is there a standard list of House human keeping genes I am trying to use the level of Expression of these genes as normalization factor to adjust RNAseq data. I googled and can see- http://www.tau.ac.il/~elieis/HKG/ however it has almost 3000 house keeping genes. I was wondering if someone has used HK in RNA seq for normalization then what will be best source. Do we used tissue specific HK?

Thanks

Answer 1

[andrew.j.skelton73]

Depends what analysis you're doing, but often in RNA seq experiments, it's not necessary to normalise to housekeeping genes. Often the most common normalisation method is scaling for library size (size factors). Check out the DESeq2 workflow in Bioconductor for gene level RNA seq analysis.