rMATS-DVR: rMATS discovery of differential variants in RNA.
BACKGROUND
RNA sequences of a gene can have single nucleotide variants (SNVs) due to single nucleotide polymorphisms (SNPs) in the genome, or RNA editing events within the RNA. By comparing RNA-seq data of a given cell type before and after a specific perturbation, we can detect and quantify SNVs in the RNA and discover SNVs with altered frequencies between distinct cellular states. Such differential variants in RNA (DVRs) may reflect allele-specific changes in gene expression or RNA processing, as well as changes in RNA editing in response to cellular perturbations or stimuli.


RESULTS
We have developed rMATS-DVR, a convenient and user-friendly software program to streamline the discovery of DVRs between two RNA-seq sample groups with replicates. rMATS-DVR combines a stringent GATK-based pipeline for calling SNVs including SNPs and RNA editing events in RNA-seq reads, with our rigorous rMATS statistical model for identifying differential isoform ratios using RNA-seq sequence count data with replicates. We applied rMATS-DVR to RNA-seq data of the human chronic myeloid leukemia cell line K562 in response to shRNA knockdown of the RNA editing enzyme ADAR1. rMATS-DVR discovered 1372 significant DVRs between knockdown and control. These DVRs encompassed known SNPs and RNA editing sites as well as novel SNVs, with the majority of DVRs corresponding to known RNA editing sites repressed after ADAR1 knockdown.


METHODS
rMATS-DVR is at https://github.com/Xinglab/rMATS-DVR .


BACKGROUND
yxing@ucla.edu.


BACKGROUND
Supplementary data are available at Bioinformatics online.
Department of Microbiology, Immunology, & Molecular Genetics, University of California Los Angeles, Los Angeles, CA, USA.
Jinkai
J
Wang
Department of Microbiology, Immunology, & Molecular Genetics, University of California Los Angeles, Los Angeles, CA, USA.
Yang
Y
Pan
Department of Microbiology, Immunology, & Molecular Genetics, University of California Los Angeles, Los Angeles, CA, USA.
Shihao
S
Shen
Department of Microbiology, Immunology, & Molecular Genetics, University of California Los Angeles, Los Angeles, CA, USA.
Lan
L
Lin
Department of Microbiology, Immunology, & Molecular Genetics, University of California Los Angeles, Los Angeles, CA, USA.
Yi
Y
Xing
D000243:Adenosine Deaminase / Q000235:genetics / Q000378:metabolism; D055785:Gene Knockdown Techniques; D006801:Humans; D020014:K562 Cells; D020641:Polymorphism, Single Nucleotide; D012313:RNA / Q000235:genetics / Q000378:metabolism*; D017393:RNA Editing; D016601:RNA-Binding Proteins / Q000235:genetics / Q000378:metabolism; D017423:Sequence Analysis, RNA / Q000379:methods*; D012984:Software
D016601:RNA-Binding Proteins; D012313:RNA; C000595356:ADAR protein, human; D000243:Adenosine Deaminase