Rna editing

Question

[RUBEM]

Hi everyone, I have data from a variant call in rna-seq and I wanted to check if some of the variants are linked to the rna editing effect, I already researched it and didn't find a satisfactory answer.

abs.

[dthorbur]

As in you found workflows but disagree with the logic? Please provide more information as we don't know what answers you've found unsatisfactory, or why.

[RUBEM]

In fact, I found more talking about the RNA editing process than tools that can perform this analysis. My question is how I could do it, whether I use bam aligned or the vcf file and which tool I can use. Sorry, I'm not that experienced in bioinformatics.

Answer 1

[HH]

I have followed methods proposed by David Liu and other researchers, such as GATK4, REDITools2, and the SAILOR pipeline. All these reference-genome-based methods without controls have significant drawbacks.

[RUBEM]

In this case, I only have rna-seq data, is it difficult to execute this SAILOR pipeline?