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Open Access Methodology article

Assessing the hodgepodge of non-mapped reads in bacterial transcriptomes: real or artifactual RNA chimeras?

Verónica Lloréns-Rico12, Luis Serrano123* and Maria Lluch-Senar12*

Author Affiliations

1 EMBL/CRG Systems Biology Research Unit, Centre for Genomic Regulation (CRG), Dr. Aiguader 88, 08003 Barcelona, Spain

2 Universitat Pompeu Fabra (UPF), Dr. Aiguader 88, 08003 Barcelona, Spain

3 Institució Catalana de Recerca i Estudis Avançats (ICREA), Pg. Lluis Companys 23, 08010 Barcelona, Spain

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BMC Genomics 2014, 15:633  doi:10.1186/1471-2164-15-633

Published: 29 July 2014

Abstract

Background

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.

Results

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 protocols