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
The best solution would be to sequence the corresponding DNA of your site of interest. If the polymorphism is still present in the genome, then it was a SNP, if not it was RNA-editing (or, if coverage not sufficient to remove this possibility, it could also just be a simple sequencing error).
Depending of your samples species, you can also have an idea about the likelyhood of being a RNA-editiing event (for instance, in mammals, RNA-editing mainly are A to I - read as A to T).
This is an interesting question and I buy the comments of Mr. Florian. However, I do have a couple of doubts that is there any consensus sequence specificity for RNA editing mechanism and when and where the RNA editing mechanism applies in the cell?
Really interesting question. With this recent report, I think the distinction between SNPs, Sequencing errors and micro exons will be discussed in depth..
http://www.ncbi.nlm.nih.gov/pubmed/25525873
Thank you Mr Tyler for your updates. Yes it should be discussed in depth as it will be a new era of research in future
Dear Mr. Tayler,
As I do not have access to the article which you had mention earlier, i request you to send me hard copy of the same. I would be very grateful to you.
Thanks
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