Do we need controls for NGS?

[janejane]

This is a kind of silly question but hope somebody can help me out here. When people do NGS, do they need to spike in controls? Can someone maybe direct me to a few papers on this?

Thanks a lot!

[mrawlins]

I haven't heard of anyone spiking in controls, though perhaps in a few less common pipelines it is used. As far as I know it's not used for RNA-Seq, SNP calling, genome assembly or ChIP-Seq. The controls most people use are simply a control condition, e.g. untreated cells for RNA-Seq, wild type for SNP calling, different IgG pull-downs for ChIP-Seq (there was some discussion about these earlier). I'm not sure what you could use as a control for genome assembly, but it may or may not require one.

[janejane]

I haven't heard of anyone spiking in controls, though perhaps in a few less common pipelines it is used. As far as I know it's not used for RNA-Seq, SNP calling, genome assembly or ChIP-Seq. The controls most people use are simply a control condition, e.g. untreated cells for RNA-Seq, wild type for SNP calling, different IgG pull-downs for ChIP-Seq (there was some discussion about these earlier). I'm not sure what you could use as a control for genome assembly, but it may or may not require one.

Thanks a lot! I am thinking of copy number variation assays or microRNAs and just a control sequence for quantification. Does this make sense? Thanks!