Question: Varscan Snp Strand Information
gravatar for GPR
5.3 years ago by
GPR300 wrote:

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.

Thanks, G.

varscan snp • 1.7k views
ADD COMMENTlink modified 5.2 years ago by dankoboldt140 • written 5.3 years ago by GPR300
gravatar for Sean Davis
5.3 years ago by
Sean Davis24k
National Institutes of Health, Bethesda, MD
Sean Davis24k wrote:

Answer to question 1: Yes

Answer to question 2: I think what you are calling "editing events" can only be called putative editing events. You would need DNA to "prove" that these are, indeed, editing events. Be sure to read this article, though, as you are dealing with a truly hard problem:

ADD COMMENTlink written 5.3 years ago by Sean Davis24k

Thanks Sean, your comments have been very useful. I have no come to realize that unlike SILAC proteomics or RNA-seq mRNA levels, RNA-editing my be a hard call in a quantitative comparative study.

ADD REPLYlink written 5.3 years ago by GPR300
gravatar for dankoboldt
5.2 years ago by
dankoboldt140 wrote:

Thanks for the question, and to Sean Davis for providing an excellent answer!

ADD COMMENTlink written 5.2 years ago by dankoboldt140
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