Distinguishing real RNA-editing event from sequencing artifact due to reverse transcription

Question

[CY]

It is known that reverse transcription during lib prep introduce relatively high amount of artifacts. In a typical RNA-editing analysis, how would we usually distinguish them from real editing events?

[ahaswer]

Start with genomic sequences of the same sample (to avoid identifying SNPs as editing events) and compare it with transcriptome sample. Also consider the fact that editing usually occurrs at first and second position of codons. The RNA-editing prediction tools may be also useful.

[CY]

We can definited filter out SNP using matched genomic sequence. However, how does genomic sequence help us distinguish RT induced artifact from real editing events? such artifacts certainly can occur in RNA sample but not in genomic sample.

[ahaswer]

Try to predict editing events based on genomic sequence using prediction tools and compare the results with corresponding transcript sequences. That will give you some insight into probable artifacts.