Hello, I am trying to compare the degree of A-to-G editing in a near-to-isogenic pair of cell lines. I have two biological replicates and have mapped with Bowtie and BWA, followed by a samtools mpileup | VarScan analysis. After this, I have used bedtools intersect to extract variants not annotated in dbSNP, but are in Alu repeats. Here is where I have some doubts, mainly two questions: QUESTION 1: In the vcf file (VarScan output),
#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT Sample1 Sample2 chrM 73 . G A PASS DP=238 GT:GQ:DP 1/1:71:121 1/1:69:117
What exactly is the meaning of
FORMAT Sample1 Sample2 GT:GQ:DP 1/1:71:121 1/1:69:117
I have higher number of editing sites "called" in sample 1 than in sample 2 in the 1st biological replicate (about 16% difference). However this difference is reversed in the 2nd biological replicate. What is the proper way of comparing the degree of RNA editing in two different samples? Is there a quantitative procedure? I have naively compared them with bedtools intersect, using or omitting option -v. Is this the correct way to go about it?
Many thanks. G.