RNA Editing data from RNA-seq

Question

[Genetics]

Does anyone help me to generate RNA editing data from raw RNA-seq data of FUNGALmodel system which has reference genome at JGI? Also would like to explain the protocol of RNA editing.

NOTE Most of the RNA editing tool I found is for human and mouse.

Thanks in advance.

[i.sudbery]

You usually need DNA sequencing data as well as RNAseq data to identify RNA editing events.

[Genetics]

I donot have DNAseq data. HAve RNAseq fastq file.

[i.sudbery]

RNA editing is detected by identifying differences between the DNA sequence and the RNAseq. If you compare your RNAseq data to the reference sequence you can find places where they differ. The RNAseq data could differ for one of three possible reasons:

1. RNA editing
2. The DNA sequence of the individual you are studying is different to the reference sequence.
3. Errors in the sequence data.

A combination of statistical models and DNA sea from a matched sample can help you distinguish these possibilities.

The REDItool you link above will do most of the steps you need (except alignment of the sequencing data to the genome). It will run on RNA data alone, but warns that it's calls may not be accurate in that case. It is not specific for mouse or human and will run on any species.

[Genetics]

Thank you so much for your kind reply and for helping a bioinformatics beginner like me.

Can I use bowtie2 tools for allignment and then use GATK/RedItool for rest of thr steps? Please let me know if you think any other tool I can use insted of bowtie2.

Also I think the reference sequence from NCBI which I am planning to refer is published by one of our collaborator and it is the same individual I am working.But I will see if i can get the DNA seq.

[Juke34]

You can use any aligner. But if you deal yourself with alignment you will loose hyperediting events except if you apply the method described by HT Porath in 2014 to retrieve the hyper edited reads.

[vil]

Hi are you talking about REDItoolDenovo

[Juke34]

What tool did you look at ?

[Genetics]

Thank you for you reply. I have fastq file(RNAseq data). As I want to use RNAItool which required input files as BAM.I have to conver fastq to BAM. Now for the following steps do the RNAItool will everything and give me the out put file?https://github.com/BioinfoUNIBA/REDItools/blob/master/README_1.md#output-files

1)Alignment and Variants Calling 2) creating reference sequence dictionary, 3) indexing of reference file, 4) handling splicing events in rna-seq data, 5) calling variants by “HaplotypeCaller” function, 6) variant selection by “SelectVariants” function, 7) variant filtration by “VariantFiltration” function 8) variant annotation

Please let me know.

[Genetics]

Hi , I have used STAR for allignment and my BAM file generated for three replicates.I am wonerding do I have to use PICARD before using REDI tool for the prediction of RNA editing sites?

Answer 1

[Juke34]

It exists plenty of tools for RNA editing analysis, some use BAM as input and some accept fastq file and will perform the alignment for you. Some look at hyper-editing some other not. Some accept DNA-seq some other not. Some will automatically detect potential SNP (to decipher from editing) some other not. Some accept extra SNP DB to mask some sites and not mix up with editing events... With some biblio you will find among others: REDItools1, Reditools2, Giremi, RNAEditor, Jacusa, Sprint, Dretools, Resic, etc. In that list Resic and RNAEditor are tools accepting Fastq files (they do the alignment). All the tools accept Bam files.

The most common tools used are RNAEditor and Reditools. The latest is Resic. Resic sounds really good on the paper, but I didn't succeed to make it work as I wanted.

[Genetics]

Thank you! I want to try Resic as it will do allingnment too for me (without loose hyperediting events) but I am unable to find a proper user manual of RESIC.