Diagnostic and filtering of genomic DNA contamination in RNA-seq data with gDNAx

Author(s): Beatriz Calvo-Serra,Robert Castelo

Affiliation(s): Universitat Pompeu Fabra



Total RNA sequencing (RNA-seq) is the most unbiased approach to characterize the whole transcriptome, and often the only available choice with degraded samples of clinical or biological interest. Unfortunately, it is also prone to genomic DNA (gDNA) contamination due to the fluctuating efficiency of the gDNA digestion step (i.e., DNase treatment), or the complete lack thereof, specially with low input samples. We present gDNAx, a Bioconductor package available at https://bioconductor.org/packages/gDNAx to quickly diagnose and quantify the presence of gDNA in RNA-seq data, and filter out reads of potential gDNA origin, thereby mitigating the impact of gDNA contamination on downstream analyses.