Hi, I have two questions...
I wanted to compare the SNPs variation due to transcription. So, I called SNPs from RNA-Seq of 321 samples of two different tissues. Please guide me which software I need to use and which pipeline needs to follow to know the variations due to transcription compare the SNPs of DNA ( I have the DNA-SNPs data from the same 321 samples).
How I can see the difference/explain the differences among GAWS-SNP target traits are common in two tissues. For example, I used two tissues and I found some target traits are commonly targeted by GWAS (SNP+expression+phenotype) in two tissues.