Assessing the hodgepodge of non-mapped reads in bacterial transcriptomes: real or artifactual RNA chimerasReport as inadecuate




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BMC Genomics

, 15:633

Transcriptomic methods

Abstract

BackgroundRNA 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.

ResultsWe 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.

ConclusionBy 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.

KeywordsChimeric RNAs Fusion transcripts RNA-seq Library preparation protocols AbbreviationsPEPaired-end

SESingle-end

THFTopHat-Fusion

CSChimeraScan

FMFusionMap

ΩseSingle-end score

ΩpePaired-end score.

Electronic supplementary materialThe online version of this article doi:10.1186-1471-2164-15-633 contains supplementary material, which is available to authorized users.

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Author: Verónica Lloréns-Rico - Luis Serrano - Maria Lluch-Senar

Source: https://link.springer.com/







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