rnaends: an R package targeted to study the exact RNA ends at the nucleotide resolution

5' and 3' RNA-end sequencing protocols have unlocked new opportunities to study aspects of RNA metabolism such as synthesis, maturation and degradation, by enabling the quantification of exact ends of RNA molecules in vivo. From RNA-Seq data that have been generated with one of the specialized protocols, it is possible to identify transcription start sites (TSS) and/or endoribonucleolytic cleavage sites, and even, in some cases, co-translational 5' to 3' degradation dynamics. Furthermore, post-transcriptional addition of ribonucleotides at the 3' end of RNA can be studied at the nucleotide resolution. While different RNA-end sequencing library protocols can vary, and have their own specificities, the generated RNA-Seq data are very similar and share common processing steps. Most importantly, the major aspect of RNA-end sequencing is that only the 5' or 3' end mapped location is of interest, contrary to conventional RNA sequencing that considers genomic ranges for gene expression analysis. This translates to a simple representation of the quantitative data as a count matrix of RNA-end location on the reference sequences. This representation seems under-exploited and is, to our knowledge, not available in a generic package focused on the analyses on the exact transcriptome ends. Here, we present the rnaends R package which is dedicated to RNA-end sequencing analysis. It offers functions for raw read pre-processing, RNA-ends mapping and quantification, RNA-ends count matrix post-processing, and further count matrix downstream analyses such as TSS identification, fast Fourier transform for signal periodic patterns analysis, or differential proportion of RNA-ends analysis. The use of rnaends is illustrated with applications in RNA metabolism studies through selected workflows on published RNA-end datasets: (i) TSS identification, (ii) ribosome translation speed and co-translational degradation, (iii) post-transcriptional modifications analysis and differential proportion analysis.