Hello, I am moving through an SNPs analysis for the first time and am now looking at my VarScan outputs, with multiple questions. My RNA-seq data is paired-end with high coverage (>200 million reads) but not strand-specific. My goal is to compare the global A-to-G editing events in a pair of isogenic cell lines. After removing the known SNPs documented in dbSNP, I have extracted variant calls in Alu repeats, and thereafter focused on the A-to-G variants, leaving behind everything else.
My questions are: 1.I understand that VarScan reports in one strand only (first strand). Does this mean that T-to-C variant calls represent A-to-G SNPs in the reverse strand? 2.I have found editing sites in a group of genes in one sample, but not in the other one being compared. Given that this finding repeats in biological replicates, is this enough to conclude the absence of a given editing in one sample but not the other? 3.How much of RNA-editing sample variation should I expect? This is, compared to total mRNA or isoform levels by RNA-seq.