RNA editing sites based on DNA seq and RNA seq

Question

[Ahiad Chen Zion]

Hi everyone.

I want to look for RNA-editing sites and Hyper editing sites on single-cell eukaryotic organism.

I have in NCBI the reference genome of that organism. Unfortunately, the DNA reference is a little different from my organism. Therefore, when I align the RNA-seq to the reference, about 20 percent of the reads do not align to the reference.

In order to overcome this issue, in addition to the RNA-seq, we create DNA-seq(both 75 bp single-end high quality).

How can I find RNA editing events using the DNA-seq? I heard about RES-SCANNER but it demands paired-end reads.

Thank you guys

[Adam]

Are those 20% unaligned reads coming after hyper-editing detection?

[Ahiad Chen Zion]

In those unaligned reads, I am looking for hyper-editing. But the alignment should be much higher