Pairs of RNA molecules transcribed from partially or entirely complementary loci are called cis-natural antisense transcripts (cis-NATs), and they play key roles in the regulation of gene expression in many organisms. A promising experimental tool for profiling sense and antisense transcription is strand-specific RNA sequencing (ssRNA-seq). To identify cis-NATs using ssRNA-seq, we developed a new computational method based on model comparison that incorporates the inherent variable efficiency of generating perfectly strand-specific libraries. Applying the method to new ssRNA-seq data from whole root and cell-type specific Arabidopsis libraries confirmed most of the known cis-NAT pairs and identified hundreds of additional cis-NAT pairs.
With an activated Bioconda channel (see 2. Set up channels), install with:
conda install r-nastiseq
and update with:
conda update r-nastiseq
A Docker container is available at https://quay.io/repository/biocontainers/r-nastiseq.