RNA-editing vs SNP

[mhkiani]

I have strand specific RNA-seq data from different samples and I'm interested to find the possible RNA editing between samples, I used CLC workbench to call variants and did the comparison and in the output I have SNP and MNP variation. My question is that how I can filter these variants to find editing sites vs SNP?

Thanks

[fanli]

I suppose you could look at nucleotide variation patterns. SNPs are generally bi-allelic whereas certain RNA edits follow specific patterns (e.g. A->I or tri-allelic). But afaik the gold standard is still to have paired DNA sequencing for your samples.

[mhkiani]

I do have paired reads and common editing in plant genome is C to U, any recommend for that?

Thanks

[NKAkers]

If you have known population SNPs, you can filter those out, and focus on those A>G sites that are common in your sequenced group. Here is an example:

http://www.nature.com/nmeth/journal/v10/n2/full/nmeth.2330.html