ReQTL

ReQTL is a software tool that performs expression quantitative trait locus (eQTL) analysis using RNA-sequencing data alone, without requiring DNA genotype information. It introduces a new method that substitutes the DNA allele count with the variant allele fraction at expressed single nucleotide variant (SNV) loci in the transcriptome (VAFRNA). This continuous measure allows for precise allele quantitation, even when RNA alleles do not scale with the genotype count. ReQTL correlates VAFRNA with gene expression to identify genetically regulated expression from RNA-seq datasets.

Topic

RNA-Seq;Gene expression;Genotype and phenotype;Functional, regulatory and non-coding RNA;Genetic variation

Detail

  • Operation: Quantification;Expression correlation analysis;Genotyping

  • Software interface: Command-line user interface

  • Language: R

  • License: Not stated

  • Cost: Free of charge

  • Version name: -

  • Credit: McCormick Genomic and Proteomic Center (MGPC), The George Washington University and NIH National Center for Advancing Translational Sciences.

  • Input: -

  • Output: -

  • Contact: Liam F Spurr lfspurr@gwmail.gwu.edu, Anelia Horvath horvatha@gwu.edu

  • Collection: -

  • Maturity: -

Publications

  • ReQTL: identifying correlations between expressed SNVs and gene expression using RNA-sequencing data.
  • Spurr LF, et al. ReQTL: identifying correlations between expressed SNVs and gene expression using RNA-sequencing data. ReQTL: identifying correlations between expressed SNVs and gene expression using RNA-sequencing data. 2020; 36:1351-1359. doi: 10.1093/bioinformatics/btz750
  • https://doi.org/10.1093/BIOINFORMATICS/BTZ750
  • PMID: 31589315
  • PMC: PMC7058180

Download and documentation

< Back to DB search