Lloréns Rico, Verónica, 1989-Serrano Pubull, Luis, 1982-Lluch-Senar, Maria 1982-2016-04-142016-04-142014Lloréns-Rico V, Serrano L, Lluch-Senar M. Assessing the hodgepodge of non-mapped reads in bacterial transcriptomes: real or artifactual RNA chimeras? BMC Genomics. 2014;15:633. DOI: 10.1186/1471-2164-15-6331471-2164http://hdl.handle.net/10230/26096Background: RNA sequencing methods have already altered our view of the extent and complexity of bacterial and eukaryotic transcriptomes, revealing rare transcript isoforms (circular RNAs, RNA chimeras) that could play an important role in their biology./nResults: We performed an analysis of chimera formation by four different computational approaches, including a custom designed pipeline, to study the transcriptomes of M. pneumoniae and P. aeruginosa, as well as mixtures of both. We found that rare transcript isoforms detected by conventional pipelines of analysis could be artifacts of the experimental procedure used in the library preparation, and that they are protocol-dependent. Conclusion: By using a customized pipeline we show that optimal library preparation protocol and the pipeline to analyze the results are crucial to identify real chimeric RNAs. Keywords: Chimeric RNAs, Fusion transcripts, RNA-seq, Library preparation protocolsapplication/pdfeng© 2014 Lloréns-Rico et al.; licensee BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly credited. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated.Genètica bacterianaRNAinfo:eu-repo/semantics/articlehttp://dx.doi.org/10.1186/1471-2164-15-633Chimeric RNAsFusion transcriptsRNA-seqLibrary preparation protocolsinfo:eu-repo/semantics/openAccess