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
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written
by
mahnazkiani
1 answer
You really need paired exome sequencing data or to otherwise be using samples that you expect to match your reference genome with few if any variants. You can find exact methods for filtering and what not if you just search "RNA editing RNAseq" in pubmed and read through the methods sections of some of the hits.
Be sure to filter for positional bias, since not doing so has caused a kerfuffle in the past.
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