CircParser : a novel streamlined pipeline for circular RNA structure and host gene prediction in non-model organisms
Peer reviewed, Journal article
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Original versionNedoluzhko, A., Sharko, F. S., Rbbani, M. G., Teslyuk, A., Konstantinidis, I. & Fernandes, J. M. de O. (2020). CircParser: a novel streamlined pipeline for circular RNA structure and host gene prediction in non-model organisms. PeerJ, 8:e8757. doi: 10.7717/peerj.8757
Circular RNAs (circRNAs) are long noncoding RNAs that play a significant role in various biological processes, including embryonic development and stress responses. These regulatory molecules can modulate microRNA activity and are involved in different molecular pathways as indirect regulators of gene expression. Thousands of circRNAs have been described in diverse taxa due to the recent advances in high throughput sequencing technologies, which led to a huge variety of total RNA sequencing being publicly available. A number of circRNA de novo and host gene prediction tools are available to date, but their ability to accurately predict circRNA host genes is limited in the case of low-quality genome assemblies or annotations. Here, we present CircParser, a simple and fast Unix/Linux pipeline that uses the outputs from the most common circular RNAs in silico prediction tools (CIRI, CIRI2, CircExplorer2, find_circ, and circFinder) to annotate circular RNAs, assigning presumptive host genes from local or public databases such as National Center for Biotechnology Information (NCBI). Also, this pipeline can discriminate circular RNAs based on their structural components (exonic, intronic, exon-intronic or intergenic) using a genome annotation file.