RNA editing

[honey]

I am trying to see if I can find possible RNA editing at genome level. Is there a reference protocol how to prepare sample for sequencing. Can I just follow the protocol of RNA- seq?
How much coverage may be optimal? Finally is there any tool available which can help me to analyze the aligned data. I know I can use Sam tool but looking for any commercial software.

Thanks for your help

[steven]

Hi,
This is interesting. Beyond RNA editing events you may also find some of these controversial RNA-DNA Differences.

I would use the GATK SNP calling module (or SAMtools) on RNA-seq data. Ideally on Re-seq data too -from the same sample- and compare.
Coverage is a tricky point because it will depend on gene expression levels. Also, I am not sure about how well would the standard SNP calling methods work on RNA-seq data.

Any idea? Has anyone tried this already?

[d17]

Anyone interested in RNA editing and RNA/DNA differences should definitely take a look at this paper:

http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0025842

[honey]

Any experience with RNA editing

I agree this is a controversial issue but I think it may be worth pursuing any expert in this area please?

[cascoamarillo]

Let me continue with this post,

I'm looking for RNA editing on a non model organism (i have a 454 ref assembly and RNA-seq experiment). I found this wonderful app: ExpEdit (http://t.caspur.it/ExpEdit/), but unfortunately it's only valid for human genome. So right now, I'm with my pileup file trying to figure out how to trim and find the points where potential RNA editing is taking place.

Any ideas / pipeline how to get this, or maybe another program that allows you to include your reference sequence.

Thanks

[vyellapa]

What alignment software are you using? Are you guys running a indel realignment step before variant calling? What I see with mpileup is that samtools misses some of the reads(I believe, those spanning exons). Im also not certain if GATK can deal wide variance in coverage of RNA data.

[rnaseek]

Here is a list of interesting papers/posts on RNA-Editing that may be worth reading and considering, especially for careful methodologies to find editing.

http://www.nature.com/news/2011/110519/full/news.2011.304.html

http://www.sciencemag.org/content/335/6074/1302.3.full

http://www.nature.com/news/rna-editing-study-under-intense-scrutiny-1.10217

http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0033720

http://genomebiology.com/2012/13/4/R26/abstract

http://www.genomesunzipped.org/2012/04/guest-post-accurate-identification-of-rna-editing-sites-from-high-throughput-sequencing-data.php