Guitar2: An improved version of the Guitar for sketching the transcriptomic view of RNA-related biological features.

Abstract

Biological elements, such as genes, exons, coding sequences, are usually expressed as genomic features based on genome-based coordinates. However, the RNA transcription landmarks are usually expressed in the form of RNA-based coordinates. To analyze the association between RNA-related genomic features and RNA transcription landmarks, some tools, such as Guitar, have been developed to convert between these two coordinate systems. However, there remain some issues, such as incomplete transcriptional structures, limitation of transcriptomic view analysis, etc. Therefore, we made corresponding improvements based on Guitar, considered the promoter, 5' cap, and 3' poly-A tail structure in the transcript, standardized the input format of RNA-related genomic features, and finally developed Guitar2. Guitar2 converts genome-based coordinates and RNA-based coordinates with a more accurate strategy. Besides, Guitar2 supports the sketching of three different transcriptional views based on the overall transcripts, messenger RNA, as well as long non-coding RNA. The analysis of m6A modification using Guitar2 shows that m6A modification is significantly enriched near the stop codon in the mRNA, which is consistent with the known results. In conclusion, Guitar2's improvement of coordinate system structure and the provision of full transcriptional view will contribute to the further analysis of RNA-related biological features. Guitar2 is now publicly available from R/Bioconductor: https://bioconductor.org/packages/release/bioc/html/Guitar.html.