validating SNPs from NGS Analysis for multiple samples

Question

[manoharankumar01]

Hi,

I have SNPs from RNA-Seq data NGS Analysis.

Which is better for validating cDNA or genomic DNA?

Is there any method available other than sanger for validating these SNPs for multiple samples?

Thanks,

[WouterDeCoster]

I wouldn't call this a bioinformatics question and this thread can/will get closed because of that, or can you convince me it is bioinformatics?

Answer 1

[Tom_L]

My colleagues (biologists) validate variants on both cDNA (to fit RNA-seq experiment at mRNA level) and genomic DNA (to determine if variant is heterozygous or homozygous) with Sanger sequencing. There also is a good reason to do both: you validate the variant with two independent experiments.

If you have detected many variants (typically >100) and want to validate them, then you may think about working with a dedicated validation platform. It shouldn't cost that much and save a lot of time (which means save money too).

Cheers