UPDATE on Mar 25, 2015:

A new version of GIREMI is released!

GitHub: https://github.com/zhqingit/giremi

What is GIREMI?

GIREMI is a method that can identify RNA editing sites using one RNA-seq data set without requiring genome sequence data.

How GIREMI works?

GIREMI calculates the mutual information (MI) of the mismatch pairs identified in the RNA-seq reads to distinguish RNA editing sites and SNPs. It also trains a generalized linear model (GLM) to achieve enhanced predictive power, which makes use of sequence bias information and the difference between the mismatch ratio of the unknown single nucleotide variants (SNVs) and the estimated allelic ratio of the gene.

Detailed information on GIREMI and citation

A paper describing GIREMI is published at Nature Methods. 

System requirement

- Currently GIREMI supports Linux 64bit (Ubuntu, Red Hat, SUSE and others) system.

- At least 8 GB of memory is required to process typical human data sets.

Dependent libraries or software

HTSlib : for accessing SAM/BAM files

Please make sure your dynamic library path in your configuration file includes the directory in which HTSlib is installed.

samtools : for generating the faidx index of reference genome sequence

Please use “samtools faidx” to generate the index before running GIREMI.

R : for general linear model training and prediction

Download:

GIREMI was implemented using a combination of R, Perl and C codes. The perl wrapper and executables can be found in GIREMI.zip. Source codes will be updated and released soon.

Please go to the GIREMI site at GitHub for the most up-to-date version:

https://github.com/zhqingit/giremi

Quickstart

Usage: giremi.pl [options] in1.bam [in2.bam [...]]

NOTE:  

-  The bam files should contain all final mapped reads in all chromosomes.

-  If multiple bam files are provided as input to GIREMI, they are handled as replicates that can be combined into one data set to generate one set of editing sites.  If it is desired that biological replicates be analyzed separately, each file should be run individually through GIREMI.

Input options:

  -f, --fasta-ref        FILE   reference genome sequence file in fasta format

                                        (NOTE: the faidx index file generated by samtools should be saved in

                                        the same directory as this fasta file)

-l, --positions       FILE   the list of all filtered SNVs after removing likely sequencing errors or      

                                      SNVs due to other artifacts (see our paper for details)

  -o, --output          FILE   write output to FILE.res

  -m, --min             INT     minimal number of total reads covering candidate editing sites            

                                         [default: 5]

  -p, --paired-end   INT    1:paired-end RNA-Seq reads; 0:single-end [default: 1]

-s, --strand          INT     0:non-strand specific RNA-Seq;

                                      1: strand-specific RNA-Seq and read 1 (first read for the paired-end

                                       reads) is sense to RNA;

                                      2: strand-specific RNA-Seq and read 1 is anti-sense to RNA

                                      [default: 0]

Required format of the file containing the list of SNVs (-l option):

column 1 :  The name of the chromosome or scaffold

column 2 : The starting position of the SNV in the chromosome or scaffold (0-based)

column 3 : The ending position of the SNV in the chromosome or scaffold (1-based)

column 4 : The name of the gene harboring this SNV; “Inte”: the SNV resides in the Intergenic region

column 5 : A flag, 1: the SNV belongs to dbSNP; 0: otherwise

column 6 : Strand (+ or -); “#” for “Inte” gene

Format of the output file:

NOTE: This output file includes a rich list of information about the SNVs.

            Not all sites in this file are predicted as RNA editing sites, see the ifRNAE field.

chr                             : Name of the chromosome or scaffold    

coordinate                 : Position of the SNVs in the chromosome or scaffold (1-based)   

strand                        : Strand information

ifSNP                         : 1, If the SNV is included in dbSNP; 0: otherwise.

gene                          : Name of the gene harboring this SNV

reference_base          : The nucleotide of this SNV in the reference chromosome (+ strand)

upstream_1base        : The upstream neighboring nucleotide of this SNV in the reference

                                     chromosome (+ strand)

downstream_1base    : The downstream neighboring nucleotide of this SNV in the reference

                                     chromosome  (+ strand)

major_base                 : The major nucleotide of the SNV in the RNA-seq data    

major_count                : Number of reads with the major nucleotide   

tot_count                     : Total number of reads covering this SNV in the RNA-Seq data  

major_ratio                  : The ratio of major nucleotide (major_count/tot_count)  

MI                                : The mutual information of this SNV if a value exists  

pvalue_mi                    : P-value from the MI test if applicable   

estimated_allelic_ratio : Estimated allelic ratio of the gene harboring this SNV

ifNEG                           : 1: this SNV was a negative control in the training data 

RNAE_t                        : Type of RNA editing or RNA-DNA mismatches (A-to-G, etc)

A,C,G,T                        : Numbers of reads with specific nucleotides at this site

ifRNAE                         : 1: the SNV is predicted as an RNA editing site based on MI analysis;

                                       2: the SNV is predicted as an RNA editing site based on GLM

                                       0: the SNV is not predicted as an RNA editing site

Contact:  zhqing _at_ ucla.edu

                gxxiao _at_ ucla.edu