Sketching the distribution of transcriptomic features on RNA transcripts with Travis coordinates

Biological features, such as, genes, transcription factor binding sites, SNPs, etc., are usually denoted with genome-based coordinates as the genomic features. While genome-based representation is usually very effective, it can be tedious to examine the distribution of RNA-related genomic features on RNA transcripts with existing tools due to the conversion and comparison between genome-based coordinates to RNA-based coordinates. We developed here an open source R package Travis for sketching the transcriptomic view of genomic features so as to facilitate the analysis of RNA-related but genome-based coordinates. Internally, Travis package extracts the coordinates relative to the landmarks of transcripts, with which the distribution of RNA-related genomic features can then be conveniently analyzed. We demonstrated the usage of Travis package in analyzing post-transcriptional RNA modifications (5-MethylCytosine and N6-MethylAdenosine) derived from high-throughput sequencing approaches (MeRIP-Seq and RNA BS-Seq). The Travis R package is now publicly available from GitHub: https://github.com/lzcyzm/Travis.